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-- ------------------------- Daniel R. Roe Laboratory of Computational Biology National Institutes of Health, NHLBI 5635 Fishers Ln, Rm T900 Rockville MD, 20852 https://www.lobos.nih.gov/lcb ------------------------------ Message: 3 Date: Wed, 12 Jul 2017 15:44:58 -0400 From: Ross Walker <ross.rosswalker.co.uk> Subject: Re: [AMBER] cudaGetDeviceCount failed unknown error AMBER16 To: AMBER Mailing List <amber.ambermd.org> Message-ID: <C99F051A-CABA-4110-8F1C-E89383FDDA3D.rosswalker.co.uk> Content-Type: text/plain; charset=us-ascii Hi Hector, Are you running AMBER 16 here with the latest patches? What does nvidia-smi report? What does nvcc -v report? You shouldn't need to do any of these hacks, especially the soft link to the libcuda.so library - that's just going to mess things up and complicate debugging more. All the best Ross > On Jul 12, 2017, at 3:16 PM, Hector Velazquez <HVelazquez.linkp.com> wrote: > > Hello AMBER development team, > > > I am trying to compile the GPU version of AMBER with an NVIDIA GTX-1080. Everything appears to be fine until I run "make test" where are all the tests fail with the following error: > > > cudaGetDeviceCount failed unknown error > > > I found the link where this error is mentioned: > > > https://mailman.ucsd.edu/pipermail/mccammon-support-l/2015/000673.html > > > However, re-running as sudo per their "quick and dirty" solution doesn't work, and the link to the longer term solution is dead. > > > My serial and parallel builds seem to be fine. > > > I also noticed the following during the "make install" step: > > > nvcc warning : The 'compute_20', 'sm_20', and 'sm_21' architectures are deprecated, and may be removed in a future release (Use -Wno-deprecated-gpu-targets to suppress warning). > > > Since it's just a warning, I don't think it matters, but I figured I would mention it just in case. > > > I did some more digging around on google and found the following link: > > > https://devtalk.nvidia.com/default/topic/617414/-solved-cuda-driver-version-is-insufficient-for-cuda-runtime-version-fedora-18-rpmfusion-driver/ > > > This thread says to do the following: > > 1. $ cd /usr/lib[64]/nvidia > 2. $ sudo ln -s libcuda.so.1 libcuda.so > 3. $ sudo ldconfig > > > I did this, but I'm still experiencing the same error. > > > Here is so information from the log from "make test" > > > > cd gb_ala3/ && ./Run.igb1_ntc1_min DPFP /storage/Programs/Amber/amber16/include/netcdf.mod > cudaGetDeviceCount failed unknown error > ./Run.igb1_ntc1_min: Program error > make[3]: [test.pmemd.cuda.gb.serial] Error 1 (ignored) > cd gb_ala3/ && ./Run.irest1_ntt0_igb1_ntc1 DPFP /storage/Programs/Amber/amber16/include/netcdf.mod > cudaGetDeviceCount failed unknown error > ./Run.irest1_ntt0_igb1_ntc1: Program error > make[3]: [test.pmemd.cuda.gb.serial] Error 1 (ignored) > cd gb_ala3/ && ./Run.irest0_ntt0_igb1_ntc1_hotstart DPFP /storage/Programs/Amber/amber16/include/netcdf.mod > cudaGetDeviceCount failed unknown error > ./Run.irest0_ntt0_igb1_ntc1_hotstart: Program error > make[3]: [test.pmemd.cuda.gb.serial] Error 1 (ignored) > > > > > > > > Thanks for your time, > > > Hector A. Velazquez > > Computational Chemistry and Cheminformatics Specialist > > NewLink Genetics > > 515-296-5555 > > Ext. 2909 > > Confidentiality Notice: This e-mail transmission contains information from NewLink Genetics that may be confidential and/or proprietary. If you are not the intended recipient, be aware that any disclosure, copying, distribution or use of the contents of this information is prohibited. Unintended distribution shall not constitute waiver of this or any other privilege and confidentiality. If you have received this e-mail transmission in error, please reply to the sender and delete the message and its contents from your system. Thank you. > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber ------------------------------ Message: 4 Date: Wed, 12 Jul 2017 17:34:02 -0400 From: Guqin Shi <shi.293.osu.edu> Subject: Re: [AMBER] Suggestions about Center and Image for multiple-molecule complex To: AMBER Mailing List <amber.ambermd.org> Message-ID: <CACUf8Hfx2f=TsmQsPuOAVF5TdmSKfAXMMG11trvVuyzpHSQqvw.mail.gmail.com> Content-Type: text/plain; charset="UTF-8" Hi Dan, I want to let you know that I have tested the new option for my latest trajectories. It works very well so far. The default "autoimage" worked well until 86 ns that conventional way couldn't work anymore in my case. Then "autoimage" with "moveanchor" were performed on the following trajectories and so far so good. However, my simulation is still ongoing. So I will keep testing and report back until my simulation is done. As to the cpptraj tests, "make check" showed that all tests are passed. So at least nothing I need to worry for now... Thanks a lot for your time and help! I am glad that my special system help raise a new option... Best, Guqin On Wed, Jul 12, 2017 at 10:39 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote: > Hi, > > On Wed, Jul 12, 2017 at 10:32 AM, Guqin Shi <shi.293.osu.edu> wrote: > > I have multiple production run trajectories which have similar problems. > I > > will test them one by one to see how things going. It might take a > while. I > > will report back hopefully by tomorrow. > > Great - all feedback is appreciated! > > > When I installed cpptraj, there were some warnings. One of them is > > "Compilation with Sander API failed: (during ./configure). Others are > > This is because your Amber installation is from Amber 14 and the > sander API has changed since then. Cpptraj's configure detects this > and disables the sander interface accordingly. > > > function warnings such as "unused variable" or "uninitialized" (during > > "make install"). I attached a file containing these warning messages. I > > These warnings have to do with the 'readline' and 'xdr' libraries and > can be safely ignored. The real check is to 'make check' in > $CPPTRAJHOME or 'make test.all' in $CPPTRAJHOME/test. > > Hope this helps, > > -Dan > > > think the latter should be ok. As to the failure with sander API, is this > > something I need to worry about considering future usage...? > > > > > > Thanks a lot for the help! Great start for today's work!! > > -Guqin > > > > On Wed, Jul 12, 2017 at 10:03 AM, Daniel Roe <daniel.r.roe.gmail.com> > wrote: > > > >> On Wed, Jul 12, 2017 at 9:55 AM, Guqin Shi <shi.293.osu.edu> wrote: > >> > Or maybe I can replace these two files under my current > >> > $AMBERHOME/AmberTools/src/cpptraj/src directory..? > >> > >> This may not work. The GitHub version of cpptraj tends to diverge from > >> the AmberTools release pretty quickly. This can also mess up future > >> AmberTools updates. Just stick with the separate install for now. > >> > >> -Dan > >> > >> > > >> > Thanks, > >> > Guqin > >> > > >> > On Wed, Jul 12, 2017 at 8:07 AM, Daniel Roe <daniel.r.roe.gmail.com> > >> wrote: > >> > > >> >> Hi, > >> >> > >> >> The new option is live: https://github.com/Amber-MD/cpptraj/pull/515 > >> >> > >> >> Just try adding the 'moveanchor' option to your 'autoimage' command. > >> >> It worked for the frames that you sent me. What it does is that when > >> >> imaging 'fixed' molecules it uses the previous molecule as the anchor > >> >> point (the first fixed molecule uses the original anchor point). This > >> >> probably will only work when molecules are both close in sequence and > >> >> geometrically close. > >> >> > >> >> Try it and let me know if it works. > >> >> > >> >> -Dan > >> >> > >> >> On Tue, Jul 11, 2017 at 4:35 PM, Guqin Shi <shi.293.osu.edu> wrote: > >> >> > Oh my god...it just made my day... > >> >> > I've been desperately looking for solutions today... for example, > I am > >> >> > currently using the topotools plugged in VMD to write coordinates > of > >> >> > replicates from adjacent cells and trying to pick out the > coordinates > >> of > >> >> an > >> >> > intact complex...meantime I am worrying about the precision, the > >> >> potential > >> >> > artifacts, and speeds in processing massive of frames... > >> >> > > >> >> > -Guqin > >> >> > > >> >> > On Tue, Jul 11, 2017 at 3:52 PM, Daniel Roe < > daniel.r.roe.gmail.com> > >> >> wrote: > >> >> > > >> >> >> I think I have a fix (really a new autoimage option) that seems to > >> >> >> work. I'm testing now and will let you know when it's live. > >> >> >> > >> >> >> -Dan > >> >> >> > >> >> >> On Tue, Jul 11, 2017 at 11:46 AM, Guqin Shi <shi.293.osu.edu> > wrote: > >> >> >> > Hi Dan, > >> >> >> > > >> >> >> > this is really unfortunate but the unwrap doesn't work either... > >> The > >> >> >> > resulting coordinates are similar to autoimage/center-image that > >> one > >> >> of > >> >> >> the > >> >> >> > molecules is still left outside... > >> >> >> > In the Amber manual, there is a notation that "this command > fails > >> when > >> >> >> the > >> >> >> > masked molecules travel more than half of the box size within a > >> single > >> >> >> > frame." Is this the reason that unwrap couldn't work either...? > >> >> >> > > >> >> >> > I uploaded the raw coordinates of pr90 and the original input > >> >> coordinates > >> >> >> > pdb file into the folder. I also uploaded the an > >> test_unwrap_copy.in > >> >> >> file > >> >> >> > which contains the commands I used for reference-unwrap... I > >> comment > >> >> out > >> >> >> > center and image commands as since the unwrap failed, center and > >> image > >> >> >> > won't help much.. > >> >> >> > > >> >> >> > If you have time, would you mind having a look at > them...Thanks... > >> >> >> > > >> >> >> > Best, > >> >> >> > Guqin > >> >> >> > > >> >> >> > On Tue, Jul 11, 2017 at 9:00 AM, Daniel Roe < > >> daniel.r.roe.gmail.com> > >> >> >> wrote: > >> >> >> > > >> >> >> >> Wow - this is certainly a challenging system to image! No one > >> >> molecule > >> >> >> >> can be considered "center" - in fact, there isn't even a region > >> of a > >> >> >> >> molecule that can be considered to be the center since when the > >> >> >> >> hexamer is formed there is a large empty space in the center > (from > >> >> >> >> looking at the system this appears to be the way it should be > >> >> >> >> assembled). > >> >> >> >> > >> >> >> >> I'll have to think about the best way to address this. In the > >> >> >> >> meantime, here is a potential workaround. You could unwrap the > >> entire > >> >> >> >> trajectory using the original input coordinates as a reference > >> >> >> >> (assuming the hexamer is "properly" formed there). You would > have > >> to > >> >> >> >> make certain you unwrap the trajectory in the right order, > i.e. in > >> >> the > >> >> >> >> same order it was simulated. You can then center on the hexamer > >> but > >> >> >> >> *only* image the water (and ions). So e.g. > >> >> >> >> > >> >> >> >> parm 1P9M_Hexamer.prmtop > >> >> >> >> reference pr90.rst7 > >> >> >> >> trajin run0.nc > >> >> >> >> trajin run1.nc > >> >> >> >> ... > >> >> >> >> unwrap reference > >> >> >> >> center :1-1330 > >> >> >> >> image :WAT,Na+ > >> >> >> >> > >> >> >> >> The idea is to keep the hexamer together by effectively never > >> imaging > >> >> >> >> it, then reimaging all the mobile stuff so it looks nice. I > think > >> >> >> >> (hope) this will work. > >> >> >> >> > >> >> >> >> Thanks for the files! > >> >> >> >> > >> >> >> >> -Dan > >> >> >> >> > >> >> >> >> On Mon, Jul 10, 2017 at 1:05 PM, Guqin Shi <shi.293.osu.edu> > >> wrote: > >> >> >> >> > Hi Dan, > >> >> >> >> > > >> >> >> >> > In addition to visualize trajectories pleasantly...my main > >> purpose > >> >> is > >> >> >> to > >> >> >> >> > get correct coordinates so that the following MMPBSA > calculation > >> >> >> could be > >> >> >> >> > carried out... (or maybe MMPBSA doesn't care about that at > >> >> all...??? > >> >> >> >> then I > >> >> >> >> > was wasting lots of my time...) > >> >> >> >> > > >> >> >> >> > I attached a prmtop with solvents stripped and a 1 ns of > >> >> >> >> nowat_coordinates > >> >> >> >> > (for the sake of file size) which I keep having problem > imaging > >> >> it... > >> >> >> ( > >> >> >> >> > https://drive.google.com/open?id= > 0B7kncIsWo85uSWJmbFBtczNtdFE) > >> >> Please > >> >> >> >> let > >> >> >> >> > me know if you feel solvated coordinates are needed... > >> >> >> >> > > >> >> >> >> > > >> >> >> >> > Thanks a lot!!! > >> >> >> >> > -Guqin > >> >> >> >> > > >> >> >> >> > On Mon, Jul 10, 2017 at 12:29 PM, Daniel Roe < > >> >> daniel.r.roe.gmail.com> > >> >> >> >> wrote: > >> >> >> >> > > >> >> >> >> >> Hi, > >> >> >> >> >> > >> >> >> >> >> (Could you send me some coordinates to go along with that > >> topology > >> >> >> >> file?) > >> >> >> >> >> > >> >> >> >> >> On Mon, Jul 10, 2017 at 12:15 PM, Guqin Shi < > shi.293.osu.edu> > >> >> wrote: > >> >> >> >> >> > at the bottom edge of box......According to the original > >> prmtop > >> >> >> files, > >> >> >> >> >> the > >> >> >> >> >> > complex sits at the center of water box, but also > meantime, > >> it > >> >> sits > >> >> >> >> along > >> >> >> >> >> > the diagonal line...It seems center-image puts molecule > along > >> >> any > >> >> >> of > >> >> >> >> the > >> >> >> >> >> > side line and that's why it just couldn't fit all back...? > >> But I > >> >> >> am so > >> >> >> >> >> > confused now as why early trajectories could be imaged > >> without > >> >> any > >> >> >> >> >> > problem... > >> >> >> >> >> > >> >> >> >> >> Re-imaging is more of an art than a science, mostly because > >> >> imaging > >> >> >> is > >> >> >> >> >> something that we do to make things "look nice". The > molecules > >> >> being > >> >> >> >> >> simulated don't care where they are absolutely, they only > care > >> >> where > >> >> >> >> >> they are with respect to other molecules. When you center on > >> one > >> >> >> >> >> molecule, you shift the coordinates of the entire system, > some > >> of > >> >> >> >> >> which move past the boundaries of your unit cell. Those > atoms > >> are > >> >> >> then > >> >> >> >> >> "wrapped" or re-imaged back inside the unit cell, which is > what > >> >> can > >> >> >> >> >> result in molecules appearing "separated". The 'autoimage' > >> command > >> >> >> >> >> tries to image in a way that keeps these molecules together > by > >> >> >> >> >> defining an anchor molecule/region (which is at the center), > >> and > >> >> >> >> >> molecules that are "fixed" to that anchor - it then tries to > >> >> minimize > >> >> >> >> >> the distance between the anchor and fixed molecules. Where > this > >> >> fails > >> >> >> >> >> is when a "wrapped" version of the system has shorter > distances > >> >> than > >> >> >> >> >> the "unwrapped version", which is typically because the > >> >> definition of > >> >> >> >> >> the anchor (center) is off. This is why the definition of > the > >> >> >> "anchor" > >> >> >> >> >> region is so crucial. > >> >> >> >> >> > >> >> >> >> >> Send me those coordinates and I'll see what can be done. > >> >> >> >> >> > >> >> >> >> >> -Dan > >> >> >> >> >> > >> >> >> >> >> > > >> >> >> >> >> > > >> >> >> >> >> > Thanks, > >> >> >> >> >> > Guqin > >> >> >> >> >> > > >> >> >> >> >> > On Mon, Jul 10, 2017 at 11:43 AM, Guqin Shi < > >> gshi.cop.ufl.edu> > >> >> >> wrote: > >> >> >> >> >> > > >> >> >> >> >> >> > >> >> >> >> >> >> On Mon, Jul 10, 2017 at 8:32 AM, Daniel Roe < > >> >> >> daniel.r.roe.gmail.com> > >> >> >> >> >> >> wrote: > >> >> >> >> >> >> > >> >> >> >> >> >>> Hi, > >> >> >> >> >> >>> > >> >> >> >> >> >>> The key for 'autoimage' is that you need to specify a > >> region > >> >> >> >> >> >>> (molecule, residue, atom, etc) that visually you want to > >> be at > >> >> >> the > >> >> >> >> >> >>> center of your unit cell; in cpptraj this is called the > >> >> >> 'anchor'. By > >> >> >> >> >> >>> default 'autoimage' tries to use the first molecule to > do > >> >> this. > >> >> >> >> >> >>> However in certain systems another choice is better. For > >> >> >> example, if > >> >> >> >> >> >>> you have a dimer then you would want to choose 1 or more > >> >> residues > >> >> >> >> that > >> >> >> >> >> >>> are near the center of the interface between the two > >> monomers > >> >> as > >> >> >> >> your > >> >> >> >> >> >>> anchor. Without seeing your system I can't make specific > >> >> >> >> >> >>> recommendations, but you could try experimenting with > >> >> different > >> >> >> >> anchor > >> >> >> >> >> >>> points. If you'd like, send me a PDB file or > >> topology/restart > >> >> >> files > >> >> >> >> of > >> >> >> >> >> >>> your system off-list and I can try to recommend an > anchor. > >> >> >> >> >> >>> > >> >> >> >> >> >>> -Dan > >> >> >> >> >> >>> > >> >> >> >> >> >>> > >> >> >> >> >> >> Hi Bill, > >> >> >> >> >> >> > >> >> >> >> >> >> Thanks for pointing out the key point of "autoimage". I > >> tried > >> >> to > >> >> >> play > >> >> >> >> >> with > >> >> >> >> >> >> autoimage-anchor a little bit by myself. I noticed that > the > >> >> mask > >> >> >> for > >> >> >> >> >> >> autoimage are molecule-wise, instead of residue-wise... > >> >> Therefore > >> >> >> >> when I > >> >> >> >> >> >> specify some center residues, cpptraj reports back with > >> error > >> >> >> (Error: > >> >> >> >> >> >> Anchor mask [:153-155] corresponds to 0 mols, should > only be > >> >> 1.) > >> >> >> and > >> >> >> >> >> then > >> >> >> >> >> >> it goes with default again... Maybe my syntax is somehow > not > >> >> >> correct? > >> >> >> >> >> >> > >> >> >> >> >> >> Also, my system is a little bit special. It is a "dimer" > and > >> >> each > >> >> >> >> >> monomer > >> >> >> >> >> >> contains three molecules. There is a hollow in between > the > >> two > >> >> >> >> dimers... > >> >> >> >> >> >> Currently in my own practice, I picked three residues on > >> each > >> >> of > >> >> >> the > >> >> >> >> >> dimer > >> >> >> >> >> >> which I think, are the closest to the center of cell > >> (143-155 & > >> >> >> >> >> 818-820). > >> >> >> >> >> >> Also, since these residues are symmetric, I am not sure > how > >> the > >> >> >> >> program > >> >> >> >> >> >> would place them in terms of direction...or maybe in this > >> case, > >> >> >> >> >> asymmetric > >> >> >> >> >> >> residues might be better...? I attached the prmtop file > >> (with > >> >> >> >> >> solvens/ions) > >> >> >> >> >> >> here on my google drive: > >> >> >> >> >> >> https://drive.google.com/open?id= > >> 0B7kncIsWo85ud1BweGJfd1h1ZXM > >> >> >> >> (Since it > >> >> >> >> >> >> is quite big so I don't think mailing list server would > >> allow > >> >> that > >> >> >> >> >> size..) > >> >> >> >> >> >> Could you also check my system to see if my choice on > >> residues > >> >> are > >> >> >> >> good > >> >> >> >> >> or > >> >> >> >> >> >> maybe another set of residues are better..? > >> >> >> >> >> >> > >> >> >> >> >> >> > >> >> >> >> >> >> Thanks a lot for your help! > >> >> >> >> >> >> -Guqin > >> >> >> >> >> >> > >> >> >> >> >> >> -- > >> >> >> >> >> >> Guqin SHI > >> >> >> >> >> >> 1345 Center Drive > >> >> >> >> >> >> College of Pharmacy > >> >> >> >> >> >> PO Box 100485 > >> >> >> >> >> >> University of Florida > >> >> >> >> >> >> Gainesville, FL 32610 > >> >> >> >> >> >> > >> >> >> >> >> > > >> >> >> >> >> > > >> >> >> >> >> > > >> >> >> >> >> > -- > >> >> >> >> >> > Guqin SHI > >> >> >> >> >> > PhD Candidate in Medicinal Chemistry and Pharmacognosy > >> >> >> >> >> > College of Pharmacy > >> >> >> >> >> > The Ohio State University > >> >> >> >> >> > Columbus, OH, 43210 > >> >> >> >> >> > _______________________________________________ > >> >> >> >> >> > AMBER mailing list > >> >> >> >> >> > AMBER.ambermd.org > >> >> >> >> >> > http://lists.ambermd.org/mailman/listinfo/amber > >> >> >> >> >> > >> >> >> >> >> > >> >> >> >> >> > >> >> >> >> >> -- > >> >> >> >> >> ------------------------- > >> >> >> >> >> Daniel R. Roe > >> >> >> >> >> Laboratory of Computational Biology > >> >> >> >> >> National Institutes of Health, NHLBI > >> >> >> >> >> 5635 Fishers Ln, Rm T900 > >> >> >> >> >> Rockville MD, 20852 > >> >> >> >> >> https://www.lobos.nih.gov/lcb > >> >> >> >> >> > >> >> >> >> >> _______________________________________________ > >> >> >> >> >> AMBER mailing list > >> >> >> >> >> AMBER.ambermd.org > >> >> >> >> >> http://lists.ambermd.org/mailman/listinfo/amber > >> >> >> >> >> > >> >> >> >> > > >> >> >> >> > > >> >> >> >> > > >> >> >> >> > -- > >> >> >> >> > Guqin SHI > >> >> >> >> > PhD Candidate in Medicinal Chemistry and Pharmacognosy > >> >> >> >> > College of Pharmacy > >> >> >> >> > The Ohio State University > >> >> >> >> > Columbus, OH, 43210 > >> >> >> >> > _______________________________________________ > >> >> >> >> > AMBER mailing list > >> >> >> >> > AMBER.ambermd.org > >> >> >> >> > http://lists.ambermd.org/mailman/listinfo/amber > >> >> >> >> > >> >> >> >> > >> >> >> >> > >> >> >> >> -- > >> >> >> >> ------------------------- > >> >> >> >> Daniel R. Roe > >> >> >> >> Laboratory of Computational Biology > >> >> >> >> National Institutes of Health, NHLBI > >> >> >> >> 5635 Fishers Ln, Rm T900 > >> >> >> >> Rockville MD, 20852 > >> >> >> >> https://www.lobos.nih.gov/lcb > >> >> >> >> > >> >> >> >> _______________________________________________ > >> >> >> >> AMBER mailing list > >> >> >> >> AMBER.ambermd.org > >> >> >> >> http://lists.ambermd.org/mailman/listinfo/amber > >> >> >> >> > >> >> >> > > >> >> >> > > >> >> >> > > >> >> >> > -- > >> >> >> > Guqin SHI > >> >> >> > PhD Candidate in Medicinal Chemistry and Pharmacognosy > >> >> >> > College of Pharmacy > >> >> >> > The Ohio State University > >> >> >> > Columbus, OH, 43210 > >> >> >> > _______________________________________________ > >> >> >> > AMBER mailing list > >> >> >> > AMBER.ambermd.org > >> >> >> > http://lists.ambermd.org/mailman/listinfo/amber > >> >> >> > >> >> >> > >> >> >> > >> >> >> -- > >> >> >> ------------------------- > >> >> >> Daniel R. Roe > >> >> >> Laboratory of Computational Biology > >> >> >> National Institutes of Health, NHLBI > >> >> >> 5635 Fishers Ln, Rm T900 > >> >> >> Rockville MD, 20852 > >> >> >> https://www.lobos.nih.gov/lcb > >> >> >> > >> >> >> _______________________________________________ > >> >> >> AMBER mailing list > >> >> >> AMBER.ambermd.org > >> >> >> http://lists.ambermd.org/mailman/listinfo/amber > >> >> >> > >> >> > > >> >> > > >> >> > > >> >> > -- > >> >> > Guqin SHI > >> >> > PhD Candidate in Medicinal Chemistry and Pharmacognosy > >> >> > College of Pharmacy > >> >> > The Ohio State University > >> >> > Columbus, OH, 43210 > >> >> > _______________________________________________ > >> >> > AMBER mailing list > >> >> > AMBER.ambermd.org > >> >> > http://lists.ambermd.org/mailman/listinfo/amber > >> >> > >> >> > >> >> > >> >> -- > >> >> ------------------------- > >> >> Daniel R. Roe > >> >> Laboratory of Computational Biology > >> >> National Institutes of Health, NHLBI > >> >> 5635 Fishers Ln, Rm T900 > >> >> Rockville MD, 20852 > >> >> https://www.lobos.nih.gov/lcb > >> >> > >> >> _______________________________________________ > >> >> AMBER mailing list > >> >> AMBER.ambermd.org > >> >> http://lists.ambermd.org/mailman/listinfo/amber > >> >> > >> > > >> > > >> > > >> > -- > >> > Guqin SHI > >> > PhD Candidate in Medicinal Chemistry and Pharmacognosy > >> > College of Pharmacy > >> > The Ohio State University > >> > Columbus, OH, 43210 > >> > _______________________________________________ > >> > AMBER mailing list > >> > AMBER.ambermd.org > >> > http://lists.ambermd.org/mailman/listinfo/amber > >> > >> > >> > >> -- > >> ------------------------- > >> Daniel R. Roe > >> Laboratory of Computational Biology > >> National Institutes of Health, NHLBI > >> 5635 Fishers Ln, Rm T900 > >> Rockville MD, 20852 > >> https://www.lobos.nih.gov/lcb > >> > >> _______________________________________________ > >> AMBER mailing list > >> AMBER.ambermd.org > >> http://lists.ambermd.org/mailman/listinfo/amber > >> > > > > > > > > -- > > Guqin SHI > > PhD Candidate in Medicinal Chemistry and Pharmacognosy > > College of Pharmacy > > The Ohio State University > > Columbus, OH, 43210 > > > > _______________________________________________ > > AMBER mailing list > > AMBER.ambermd.org > > http://lists.ambermd.org/mailman/listinfo/amber > > > > > > -- > ------------------------- > Daniel R. Roe > Laboratory of Computational Biology > National Institutes of Health, NHLBI > 5635 Fishers Ln, Rm T900 > Rockville MD, 20852 > https://www.lobos.nih.gov/lcb > > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber > -- Guqin SHI PhD Candidate in Medicinal Chemistry and Pharmacognosy College of Pharmacy The Ohio State University Columbus, OH, 43210 ------------------------------ Message: 5 Date: Wed, 12 Jul 2017 14:37:58 -0700 From: Bill Ross <ross.cgl.ucsf.edu> Subject: Re: [AMBER] Suggestions about Center and Image for multiple-molecule complex To: amber.ambermd.org Message-ID: <2c81c86f-7c10-1e34-384b-fa9d1314e0ec.cgl.ucsf.edu> Content-Type: text/plain; charset=utf-8; format=flowed I still wonder if my idea would be a more general solution, requiring no thought on the user's part. Bill On 7/12/17 2:34 PM, Guqin Shi wrote: > Hi Dan, > > I want to let you know that I have tested the new option for my latest > trajectories. It works very well so far. > The default "autoimage" worked well until 86 ns that conventional way > couldn't work anymore in my case. Then "autoimage" with "moveanchor" were > performed on the following trajectories and so far so good. However, my > simulation is still ongoing. So I will keep testing and report back until > my simulation is done. > > As to the cpptraj tests, "make check" showed that all tests are passed. So > at least nothing I need to worry for now... > > > Thanks a lot for your time and help! I am glad that my special system help > raise a new option... > > Best, > Guqin > > On Wed, Jul 12, 2017 at 10:39 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote: > >> Hi, >> >> On Wed, Jul 12, 2017 at 10:32 AM, Guqin Shi <shi.293.osu.edu> wrote: >>> I have multiple production run trajectories which have similar problems. >> I >>> will test them one by one to see how things going. It might take a >> while. I >>> will report back hopefully by tomorrow. >> Great - all feedback is appreciated! >> >>> When I installed cpptraj, there were some warnings. One of them is >>> "Compilation with Sander API failed: (during ./configure). Others are >> This is because your Amber installation is from Amber 14 and the >> sander API has changed since then. Cpptraj's configure detects this >> and disables the sander interface accordingly. >> >>> function warnings such as "unused variable" or "uninitialized" (during >>> "make install"). I attached a file containing these warning messages. I >> These warnings have to do with the 'readline' and 'xdr' libraries and >> can be safely ignored. The real check is to 'make check' in >> $CPPTRAJHOME or 'make test.all' in $CPPTRAJHOME/test. >> >> Hope this helps, >> >> -Dan >> >>> think the latter should be ok. As to the failure with sander API, is this >>> something I need to worry about considering future usage...? >>> >>> >>> Thanks a lot for the help! Great start for today's work!! >>> -Guqin >>> >>> On Wed, Jul 12, 2017 at 10:03 AM, Daniel Roe <daniel.r.roe.gmail.com> >> wrote: >>>> On Wed, Jul 12, 2017 at 9:55 AM, Guqin Shi <shi.293.osu.edu> wrote: >>>>> Or maybe I can replace these two files under my current >>>>> $AMBERHOME/AmberTools/src/cpptraj/src directory..? >>>> This may not work. The GitHub version of cpptraj tends to diverge from >>>> the AmberTools release pretty quickly. This can also mess up future >>>> AmberTools updates. Just stick with the separate install for now. >>>> >>>> -Dan >>>> >>>>> Thanks, >>>>> Guqin >>>>> >>>>> On Wed, Jul 12, 2017 at 8:07 AM, Daniel Roe <daniel.r.roe.gmail.com> >>>> wrote: >>>>>> Hi, >>>>>> >>>>>> The new option is live: https://github.com/Amber-MD/cpptraj/pull/515 >>>>>> >>>>>> Just try adding the 'moveanchor' option to your 'autoimage' command. >>>>>> It worked for the frames that you sent me. What it does is that when >>>>>> imaging 'fixed' molecules it uses the previous molecule as the anchor >>>>>> point (the first fixed molecule uses the original anchor point). This >>>>>> probably will only work when molecules are both close in sequence and >>>>>> geometrically close. >>>>>> >>>>>> Try it and let me know if it works. >>>>>> >>>>>> -Dan >>>>>> >>>>>> On Tue, Jul 11, 2017 at 4:35 PM, Guqin Shi <shi.293.osu.edu> wrote: >>>>>>> Oh my god...it just made my day... >>>>>>> I've been desperately looking for solutions today... for example, >> I am >>>>>>> currently using the topotools plugged in VMD to write coordinates >> of >>>>>>> replicates from adjacent cells and trying to pick out the >> coordinates >>>> of >>>>>> an >>>>>>> intact complex...meantime I am worrying about the precision, the >>>>>> potential >>>>>>> artifacts, and speeds in processing massive of frames... >>>>>>> >>>>>>> -Guqin >>>>>>> >>>>>>> On Tue, Jul 11, 2017 at 3:52 PM, Daniel Roe < >> daniel.r.roe.gmail.com> >>>>>> wrote: >>>>>>>> I think I have a fix (really a new autoimage option) that seems to >>>>>>>> work. I'm testing now and will let you know when it's live. >>>>>>>> >>>>>>>> -Dan >>>>>>>> >>>>>>>> On Tue, Jul 11, 2017 at 11:46 AM, Guqin Shi <shi.293.osu.edu> >> wrote: >>>>>>>>> Hi Dan, >>>>>>>>> >>>>>>>>> this is really unfortunate but the unwrap doesn't work either... >>>> The >>>>>>>>> resulting coordinates are similar to autoimage/center-image that >>>> one >>>>>> of >>>>>>>> the >>>>>>>>> molecules is still left outside... >>>>>>>>> In the Amber manual, there is a notation that "this command >> fails >>>> when >>>>>>>> the >>>>>>>>> masked molecules travel more than half of the box size within a >>>> single >>>>>>>>> frame." Is this the reason that unwrap couldn't work either...? >>>>>>>>> >>>>>>>>> I uploaded the raw coordinates of pr90 and the original input >>>>>> coordinates >>>>>>>>> pdb file into the folder. I also uploaded the an >>>> test_unwrap_copy.in >>>>>>>> file >>>>>>>>> which contains the commands I used for reference-unwrap... I >>>> comment >>>>>> out >>>>>>>>> center and image commands as since the unwrap failed, center and >>>> image >>>>>>>>> won't help much.. >>>>>>>>> >>>>>>>>> If you have time, would you mind having a look at >> them...Thanks... >>>>>>>>> Best, >>>>>>>>> Guqin >>>>>>>>> >>>>>>>>> On Tue, Jul 11, 2017 at 9:00 AM, Daniel Roe < >>>> daniel.r.roe.gmail.com> >>>>>>>> wrote: >>>>>>>>>> Wow - this is certainly a challenging system to image! No one >>>>>> molecule >>>>>>>>>> can be considered "center" - in fact, there isn't even a region >>>> of a >>>>>>>>>> molecule that can be considered to be the center since when the >>>>>>>>>> hexamer is formed there is a large empty space in the center >> (from >>>>>>>>>> looking at the system this appears to be the way it should be >>>>>>>>>> assembled). >>>>>>>>>> >>>>>>>>>> I'll have to think about the best way to address this. In the >>>>>>>>>> meantime, here is a potential workaround. You could unwrap the >>>> entire >>>>>>>>>> trajectory using the original input coordinates as a reference >>>>>>>>>> (assuming the hexamer is "properly" formed there). You would >> have >>>> to >>>>>>>>>> make certain you unwrap the trajectory in the right order, >> i.e. in >>>>>> the >>>>>>>>>> same order it was simulated. You can then center on the hexamer >>>> but >>>>>>>>>> *only* image the water (and ions). So e.g. >>>>>>>>>> >>>>>>>>>> parm 1P9M_Hexamer.prmtop >>>>>>>>>> reference pr90.rst7 >>>>>>>>>> trajin run0.nc >>>>>>>>>> trajin run1.nc >>>>>>>>>> ... >>>>>>>>>> unwrap reference >>>>>>>>>> center :1-1330 >>>>>>>>>> image :WAT,Na+ >>>>>>>>>> >>>>>>>>>> The idea is to keep the hexamer together by effectively never >>>> imaging >>>>>>>>>> it, then reimaging all the mobile stuff so it looks nice. I >> think >>>>>>>>>> (hope) this will work. >>>>>>>>>> >>>>>>>>>> Thanks for the files! >>>>>>>>>> >>>>>>>>>> -Dan >>>>>>>>>> >>>>>>>>>> On Mon, Jul 10, 2017 at 1:05 PM, Guqin Shi <shi.293.osu.edu> >>>> wrote: >>>>>>>>>>> Hi Dan, >>>>>>>>>>> >>>>>>>>>>> In addition to visualize trajectories pleasantly...my main >>>> purpose >>>>>> is >>>>>>>> to >>>>>>>>>>> get correct coordinates so that the following MMPBSA >> calculation >>>>>>>> could be >>>>>>>>>>> carried out... (or maybe MMPBSA doesn't care about that at >>>>>> all...??? >>>>>>>>>> then I >>>>>>>>>>> was wasting lots of my time...) >>>>>>>>>>> >>>>>>>>>>> I attached a prmtop with solvents stripped and a 1 ns of >>>>>>>>>> nowat_coordinates >>>>>>>>>>> (for the sake of file size) which I keep having problem >> imaging >>>>>> it... >>>>>>>> ( >>>>>>>>>>> https://drive.google.com/open?id= >> 0B7kncIsWo85uSWJmbFBtczNtdFE) >>>>>> Please >>>>>>>>>> let >>>>>>>>>>> me know if you feel solvated coordinates are needed... >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> Thanks a lot!!! >>>>>>>>>>> -Guqin >>>>>>>>>>> >>>>>>>>>>> On Mon, Jul 10, 2017 at 12:29 PM, Daniel Roe < >>>>>> daniel.r.roe.gmail.com> >>>>>>>>>> wrote: >>>>>>>>>>>> Hi, >>>>>>>>>>>> >>>>>>>>>>>> (Could you send me some coordinates to go along with that >>>> topology >>>>>>>>>> file?) >>>>>>>>>>>> On Mon, Jul 10, 2017 at 12:15 PM, Guqin Shi < >> shi.293.osu.edu> >>>>>> wrote: >>>>>>>>>>>>> at the bottom edge of box......According to the original >>>> prmtop >>>>>>>> files, >>>>>>>>>>>> the >>>>>>>>>>>>> complex sits at the center of water box, but also >> meantime, >>>> it >>>>>> sits >>>>>>>>>> along >>>>>>>>>>>>> the diagonal line...It seems center-image puts molecule >> along >>>>>> any >>>>>>>> of >>>>>>>>>> the >>>>>>>>>>>>> side line and that's why it just couldn't fit all back...? >>>> But I >>>>>>>> am so >>>>>>>>>>>>> confused now as why early trajectories could be imaged >>>> without >>>>>> any >>>>>>>>>>>>> problem... >>>>>>>>>>>> Re-imaging is more of an art than a science, mostly because >>>>>> imaging >>>>>>>> is >>>>>>>>>>>> something that we do to make things "look nice". The >> molecules >>>>>> being >>>>>>>>>>>> simulated don't care where they are absolutely, they only >> care >>>>>> where >>>>>>>>>>>> they are with respect to other molecules. When you center on >>>> one >>>>>>>>>>>> molecule, you shift the coordinates of the entire system, >> some >>>> of >>>>>>>>>>>> which move past the boundaries of your unit cell. Those >> atoms >>>> are >>>>>>>> then >>>>>>>>>>>> "wrapped" or re-imaged back inside the unit cell, which is >> what >>>>>> can >>>>>>>>>>>> result in molecules appearing "separated". The 'autoimage' >>>> command >>>>>>>>>>>> tries to image in a way that keeps these molecules together >> by >>>>>>>>>>>> defining an anchor molecule/region (which is at the center), >>>> and >>>>>>>>>>>> molecules that are "fixed" to that anchor - it then tries to >>>>>> minimize >>>>>>>>>>>> the distance between the anchor and fixed molecules. Where >> this >>>>>> fails >>>>>>>>>>>> is when a "wrapped" version of the system has shorter >> distances >>>>>> than >>>>>>>>>>>> the "unwrapped version", which is typically because the >>>>>> definition of >>>>>>>>>>>> the anchor (center) is off. This is why the definition of >> the >>>>>>>> "anchor" >>>>>>>>>>>> region is so crucial. >>>>>>>>>>>> >>>>>>>>>>>> Send me those coordinates and I'll see what can be done. >>>>>>>>>>>> >>>>>>>>>>>> -Dan >>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> Thanks, >>>>>>>>>>>>> Guqin >>>>>>>>>>>>> >>>>>>>>>>>>> On Mon, Jul 10, 2017 at 11:43 AM, Guqin Shi < >>>> gshi.cop.ufl.edu> >>>>>>>> wrote: >>>>>>>>>>>>>> On Mon, Jul 10, 2017 at 8:32 AM, Daniel Roe < >>>>>>>> daniel.r.roe.gmail.com> >>>>>>>>>>>>>> wrote: >>>>>>>>>>>>>> >>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> The key for 'autoimage' is that you need to specify a >>>> region >>>>>>>>>>>>>>> (molecule, residue, atom, etc) that visually you want to >>>> be at >>>>>>>> the >>>>>>>>>>>>>>> center of your unit cell; in cpptraj this is called the >>>>>>>> 'anchor'. By >>>>>>>>>>>>>>> default 'autoimage' tries to use the first molecule to >> do >>>>>> this. >>>>>>>>>>>>>>> However in certain systems another choice is better. For >>>>>>>> example, if >>>>>>>>>>>>>>> you have a dimer then you would want to choose 1 or more >>>>>> residues >>>>>>>>>> that >>>>>>>>>>>>>>> are near the center of the interface between the two >>>> monomers >>>>>> as >>>>>>>>>> your >>>>>>>>>>>>>>> anchor. Without seeing your system I can't make specific >>>>>>>>>>>>>>> recommendations, but you could try experimenting with >>>>>> different >>>>>>>>>> anchor >>>>>>>>>>>>>>> points. If you'd like, send me a PDB file or >>>> topology/restart >>>>>>>> files >>>>>>>>>> of >>>>>>>>>>>>>>> your system off-list and I can try to recommend an >> anchor. >>>>>>>>>>>>>>> -Dan >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>> Hi Bill, >>>>>>>>>>>>>> >>>>>>>>>>>>>> Thanks for pointing out the key point of "autoimage". I >>>> tried >>>>>> to >>>>>>>> play >>>>>>>>>>>> with >>>>>>>>>>>>>> autoimage-anchor a little bit by myself. I noticed that >> the >>>>>> mask >>>>>>>> for >>>>>>>>>>>>>> autoimage are molecule-wise, instead of residue-wise... >>>>>> Therefore >>>>>>>>>> when I >>>>>>>>>>>>>> specify some center residues, cpptraj reports back with >>>> error >>>>>>>> (Error: >>>>>>>>>>>>>> Anchor mask [:153-155] corresponds to 0 mols, should >> only be >>>>>> 1.) >>>>>>>> and >>>>>>>>>>>> then >>>>>>>>>>>>>> it goes with default again... Maybe my syntax is somehow >> not >>>>>>>> correct? >>>>>>>>>>>>>> Also, my system is a little bit special. It is a "dimer" >> and >>>>>> each >>>>>>>>>>>> monomer >>>>>>>>>>>>>> contains three molecules. There is a hollow in between >> the >>>> two >>>>>>>>>> dimers... >>>>>>>>>>>>>> Currently in my own practice, I picked three residues on >>>> each >>>>>> of >>>>>>>> the >>>>>>>>>>>> dimer >>>>>>>>>>>>>> which I think, are the closest to the center of cell >>>> (143-155 & >>>>>>>>>>>> 818-820). >>>>>>>>>>>>>> Also, since these residues are symmetric, I am not sure >> how >>>> the >>>>>>>>>> program >>>>>>>>>>>>>> would place them in terms of direction...or maybe in this >>>> case, >>>>>>>>>>>> asymmetric >>>>>>>>>>>>>> residues might be better...? I attached the prmtop file >>>> (with >>>>>>>>>>>> solvens/ions) >>>>>>>>>>>>>> here on my google drive: >>>>>>>>>>>>>> https://drive.google.com/open?id= >>>> 0B7kncIsWo85ud1BweGJfd1h1ZXM >>>>>>>>>> (Since it >>>>>>>>>>>>>> is quite big so I don't think mailing list server would >>>> allow >>>>>> that >>>>>>>>>>>> size..) >>>>>>>>>>>>>> Could you also check my system to see if my choice on >>>> residues >>>>>> are >>>>>>>>>> good >>>>>>>>>>>> or >>>>>>>>>>>>>> maybe another set of residues are better..? >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> Thanks a lot for your help! >>>>>>>>>>>>>> -Guqin >>>>>>>>>>>>>> >>>>>>>>>>>>>> -- >>>>>>>>>>>>>> Guqin SHI >>>>>>>>>>>>>> 1345 Center Drive >>>>>>>>>>>>>> College of Pharmacy >>>>>>>>>>>>>> PO Box 100485 >>>>>>>>>>>>>> University of Florida >>>>>>>>>>>>>> Gainesville, FL 32610 >>>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> -- >>>>>>>>>>>>> Guqin SHI >>>>>>>>>>>>> PhD Candidate in Medicinal Chemistry and Pharmacognosy >>>>>>>>>>>>> College of Pharmacy >>>>>>>>>>>>> The Ohio State University >>>>>>>>>>>>> Columbus, OH, 43210 >>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>> AMBER mailing list >>>>>>>>>>>>> AMBER.ambermd.org >>>>>>>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> -- >>>>>>>>>>>> ------------------------- >>>>>>>>>>>> Daniel R. Roe >>>>>>>>>>>> Laboratory of Computational Biology >>>>>>>>>>>> National Institutes of Health, NHLBI >>>>>>>>>>>> 5635 Fishers Ln, Rm T900 >>>>>>>>>>>> Rockville MD, 20852 >>>>>>>>>>>> https://www.lobos.nih.gov/lcb >>>>>>>>>>>> >>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>> AMBER mailing list >>>>>>>>>>>> AMBER.ambermd.org >>>>>>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber >>>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> -- >>>>>>>>>>> Guqin SHI >>>>>>>>>>> PhD Candidate in Medicinal Chemistry and Pharmacognosy >>>>>>>>>>> College of Pharmacy >>>>>>>>>>> The Ohio State University >>>>>>>>>>> Columbus, OH, 43210 >>>>>>>>>>> _______________________________________________ >>>>>>>>>>> AMBER mailing list >>>>>>>>>>> AMBER.ambermd.org >>>>>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> -- >>>>>>>>>> ------------------------- >>>>>>>>>> Daniel R. Roe >>>>>>>>>> Laboratory of Computational Biology >>>>>>>>>> National Institutes of Health, NHLBI >>>>>>>>>> 5635 Fishers Ln, Rm T900 >>>>>>>>>> Rockville MD, 20852 >>>>>>>>>> https://www.lobos.nih.gov/lcb >>>>>>>>>> >>>>>>>>>> _______________________________________________ >>>>>>>>>> AMBER mailing list >>>>>>>>>> AMBER.ambermd.org >>>>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber >>>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> -- >>>>>>>>> Guqin SHI >>>>>>>>> PhD Candidate in Medicinal Chemistry and Pharmacognosy >>>>>>>>> College of Pharmacy >>>>>>>>> The Ohio State University >>>>>>>>> Columbus, OH, 43210 >>>>>>>>> _______________________________________________ >>>>>>>>> AMBER mailing list >>>>>>>>> AMBER.ambermd.org >>>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber >>>>>>>> >>>>>>>> >>>>>>>> -- >>>>>>>> ------------------------- >>>>>>>> Daniel R. Roe >>>>>>>> Laboratory of Computational Biology >>>>>>>> National Institutes of Health, NHLBI >>>>>>>> 5635 Fishers Ln, Rm T900 >>>>>>>> Rockville MD, 20852 >>>>>>>> https://www.lobos.nih.gov/lcb >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> AMBER mailing list >>>>>>>> AMBER.ambermd.org >>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber >>>>>>>> >>>>>>> >>>>>>> >>>>>>> -- >>>>>>> Guqin SHI >>>>>>> PhD Candidate in Medicinal Chemistry and Pharmacognosy >>>>>>> College of Pharmacy >>>>>>> The Ohio State University >>>>>>> Columbus, OH, 43210 >>>>>>> _______________________________________________ >>>>>>> AMBER mailing list >>>>>>> AMBER.ambermd.org >>>>>>> http://lists.ambermd.org/mailman/listinfo/amber >>>>>> >>>>>> >>>>>> -- >>>>>> ------------------------- >>>>>> Daniel R. Roe >>>>>> Laboratory of Computational Biology >>>>>> National Institutes of Health, NHLBI >>>>>> 5635 Fishers Ln, Rm T900 >>>>>> Rockville MD, 20852 >>>>>> https://www.lobos.nih.gov/lcb >>>>>> >>>>>> _______________________________________________ >>>>>> AMBER mailing list >>>>>> AMBER.ambermd.org >>>>>> http://lists.ambermd.org/mailman/listinfo/amber >>>>>> >>>>> >>>>> >>>>> -- >>>>> Guqin SHI >>>>> PhD Candidate in Medicinal Chemistry and Pharmacognosy >>>>> College of Pharmacy >>>>> The Ohio State University >>>>> Columbus, OH, 43210 >>>>> _______________________________________________ >>>>> AMBER mailing list >>>>> AMBER.ambermd.org >>>>> http://lists.ambermd.org/mailman/listinfo/amber >>>> >>>> >>>> -- >>>> ------------------------- >>>> Daniel R. Roe >>>> Laboratory of Computational Biology >>>> National Institutes of Health, NHLBI >>>> 5635 Fishers Ln, Rm T900 >>>> Rockville MD, 20852 >>>> https://www.lobos.nih.gov/lcb >>>> >>>> _______________________________________________ >>>> AMBER mailing list >>>> AMBER.ambermd.org >>>> http://lists.ambermd.org/mailman/listinfo/amber >>>> >>> >>> >>> -- >>> Guqin SHI >>> PhD Candidate in Medicinal Chemistry and Pharmacognosy >>> College of Pharmacy >>> The Ohio State University >>> Columbus, OH, 43210 >>> >>> _______________________________________________ >>> AMBER mailing list >>> AMBER.ambermd.org >>> http://lists.ambermd.org/mailman/listinfo/amber >>> >> >> >> -- >> ------------------------- >> Daniel R. Roe >> Laboratory of Computational Biology >> National Institutes of Health, NHLBI >> 5635 Fishers Ln, Rm T900 >> Rockville MD, 20852 >> https://www.lobos.nih.gov/lcb >> >> _______________________________________________ >> AMBER mailing list >> AMBER.ambermd.org >> http://lists.ambermd.org/mailman/listinfo/amber >> > > ------------------------------ Message: 6 Date: Wed, 12 Jul 2017 14:46:54 -0700 From: Bill Ross <ross.cgl.ucsf.edu> Subject: [AMBER] A DNA-based short-term memory for biological deep learning To: AMBER Mailing List <amber.ambermd.org> Message-ID: <b74a13d4-21f4-aeb6-b0e9-abc8d825f46e.cgl.ucsf.edu> Content-Type: text/plain; charset=utf-8; format=flowed Here's a far-fetched but tantalizing prospect that I have revived in light of deep learning research: https://www.reddit.com/r/MachineLearning/comments/6mnqwn/d_a_dnabased_cellular_memory_system_for_deep/ Bill ------------------------------ Message: 7 Date: Wed, 12 Jul 2017 17:54:34 -0400 From: Guqin Shi <shi.293.osu.edu> Subject: Re: [AMBER] Suggestions about Center and Image for multiple-molecule complex To: AMBER Mailing List <amber.ambermd.org> Message-ID: <CACUf8HdP+UMaNHmxUmN4UCBpjSA_3pMNnqqcy3zPQLHrgKS+gA.mail.gmail.com> Content-Type: text/plain; charset="UTF-8" Hi Bill, Thanks for your suggestion on this problem. Dan helped add a new option and seemingly solved the problem. (I am writing this email and saw your new reply just came in.) But I did go to check the "pytraj" and I am glad I did so. Previously I used cpptraj to get results and write separate python script to process or plot the data; but with pytraj it seems two steps could be merged into one. Although I didn't utilize pytraj to solve this problem but it's good to know it. As for your previous suggestion on image minimizer, I kinda get your idea. Because while Dan was developing the new option, I was using topotools in vmd to write protein coordinates from adjacent cells and picked out an intact hexamer manually. This is basically (from my understanding...) what you were mentioning: get translated images/coordinates and the molecules with the closest distance should theoretically be in the "correct" complex... But I don't know for this method, how general it could be and how efficient it will be (considering the translation have to be done on all axes and iterations will be done on all mols/atoms...) I have no experience or idea. But I would love to follow up with updates if future cpptraj would have such changes. Best, Guqin On Wed, Jul 12, 2017 at 5:37 PM, Bill Ross <ross.cgl.ucsf.edu> wrote: > I still wonder if my idea would be a more general solution, requiring no > thought on the user's part. > > Bill > > > On 7/12/17 2:34 PM, Guqin Shi wrote: > > Hi Dan, > > > > I want to let you know that I have tested the new option for my latest > > trajectories. It works very well so far. > > The default "autoimage" worked well until 86 ns that conventional way > > couldn't work anymore in my case. Then "autoimage" with "moveanchor" were > > performed on the following trajectories and so far so good. However, my > > simulation is still ongoing. So I will keep testing and report back until > > my simulation is done. > > > > As to the cpptraj tests, "make check" showed that all tests are passed. > So > > at least nothing I need to worry for now... > > > > > > Thanks a lot for your time and help! I am glad that my special system > help > > raise a new option... > > > > Best, > > Guqin > > > > On Wed, Jul 12, 2017 at 10:39 AM, Daniel Roe <daniel.r.roe.gmail.com> > wrote: > > > >> Hi, > >> > >> On Wed, Jul 12, 2017 at 10:32 AM, Guqin Shi <shi.293.osu.edu> wrote: > >>> I have multiple production run trajectories which have similar > problems. > >> I > >>> will test them one by one to see how things going. It might take a > >> while. I > >>> will report back hopefully by tomorrow. > >> Great - all feedback is appreciated! > >> > >>> When I installed cpptraj, there were some warnings. One of them is > >>> "Compilation with Sander API failed: (during ./configure). Others are > >> This is because your Amber installation is from Amber 14 and the > >> sander API has changed since then. Cpptraj's configure detects this > >> and disables the sander interface accordingly. > >> > >>> function warnings such as "unused variable" or "uninitialized" (during > >>> "make install"). I attached a file containing these warning messages. I > >> These warnings have to do with the 'readline' and 'xdr' libraries and > >> can be safely ignored. The real check is to 'make check' in > >> $CPPTRAJHOME or 'make test.all' in $CPPTRAJHOME/test. > >> > >> Hope this helps, > >> > >> -Dan > >> > >>> think the latter should be ok. As to the failure with sander API, is > this > >>> something I need to worry about considering future usage...? > >>> > >>> > >>> Thanks a lot for the help! Great start for today's work!! > >>> -Guqin > >>> > >>> On Wed, Jul 12, 2017 at 10:03 AM, Daniel Roe <daniel.r.roe.gmail.com> > >> wrote: > >>>> On Wed, Jul 12, 2017 at 9:55 AM, Guqin Shi <shi.293.osu.edu> wrote: > >>>>> Or maybe I can replace these two files under my current > >>>>> $AMBERHOME/AmberTools/src/cpptraj/src directory..? > >>>> This may not work. The GitHub version of cpptraj tends to diverge from > >>>> the AmberTools release pretty quickly. This can also mess up future > >>>> AmberTools updates. Just stick with the separate install for now. > >>>> > >>>> -Dan > >>>> > >>>>> Thanks, > >>>>> Guqin > >>>>> > >>>>> On Wed, Jul 12, 2017 at 8:07 AM, Daniel Roe <daniel.r.roe.gmail.com> > >>>> wrote: > >>>>>> Hi, > >>>>>> > >>>>>> The new option is live: https://github.com/Amber-MD/ > cpptraj/pull/515 > >>>>>> > >>>>>> Just try adding the 'moveanchor' option to your 'autoimage' command. > >>>>>> It worked for the frames that you sent me. What it does is that when > >>>>>> imaging 'fixed' molecules it uses the previous molecule as the > anchor > >>>>>> point (the first fixed molecule uses the original anchor point). > This > >>>>>> probably will only work when molecules are both close in sequence > and > >>>>>> geometrically close. > >>>>>> > >>>>>> Try it and let me know if it works. > >>>>>> > >>>>>> -Dan > >>>>>> > >>>>>> On Tue, Jul 11, 2017 at 4:35 PM, Guqin Shi <shi.293.osu.edu> wrote: > >>>>>>> Oh my god...it just made my day... > >>>>>>> I've been desperately looking for solutions today... for example, > >> I am > >>>>>>> currently using the topotools plugged in VMD to write coordinates > >> of > >>>>>>> replicates from adjacent cells and trying to pick out the > >> coordinates > >>>> of > >>>>>> an > >>>>>>> intact complex...meantime I am worrying about the precision, the > >>>>>> potential > >>>>>>> artifacts, and speeds in processing massive of frames... > >>>>>>> > >>>>>>> -Guqin > >>>>>>> > >>>>>>> On Tue, Jul 11, 2017 at 3:52 PM, Daniel Roe < > >> daniel.r.roe.gmail.com> > >>>>>> wrote: > >>>>>>>> I think I have a fix (really a new autoimage option) that seems to > >>>>>>>> work. I'm testing now and will let you know when it's live. > >>>>>>>> > >>>>>>>> -Dan > >>>>>>>> > >>>>>>>> On Tue, Jul 11, 2017 at 11:46 AM, Guqin Shi <shi.293.osu.edu> > >> wrote: > >>>>>>>>> Hi Dan, > >>>>>>>>> > >>>>>>>>> this is really unfortunate but the unwrap doesn't work either... > >>>> The > >>>>>>>>> resulting coordinates are similar to autoimage/center-image that > >>>> one > >>>>>> of > >>>>>>>> the > >>>>>>>>> molecules is still left outside... > >>>>>>>>> In the Amber manual, there is a notation that "this command > >> fails > >>>> when > >>>>>>>> the > >>>>>>>>> masked molecules travel more than half of the box size within a > >>>> single > >>>>>>>>> frame." Is this the reason that unwrap couldn't work either...? > >>>>>>>>> > >>>>>>>>> I uploaded the raw coordinates of pr90 and the original input > >>>>>> coordinates > >>>>>>>>> pdb file into the folder. I also uploaded the an > >>>> test_unwrap_copy.in > >>>>>>>> file > >>>>>>>>> which contains the commands I used for reference-unwrap... I > >>>> comment > >>>>>> out > >>>>>>>>> center and image commands as since the unwrap failed, center and > >>>> image > >>>>>>>>> won't help much.. > >>>>>>>>> > >>>>>>>>> If you have time, would you mind having a look at > >> them...Thanks... > >>>>>>>>> Best, > >>>>>>>>> Guqin > >>>>>>>>> > >>>>>>>>> On Tue, Jul 11, 2017 at 9:00 AM, Daniel Roe < > >>>> daniel.r.roe.gmail.com> > >>>>>>>> wrote: > >>>>>>>>>> Wow - this is certainly a challenging system to image! No one > >>>>>> molecule > >>>>>>>>>> can be considered "center" - in fact, there isn't even a region > >>>> of a > >>>>>>>>>> molecule that can be considered to be the center since when the > >>>>>>>>>> hexamer is formed there is a large empty space in the center > >> (from > >>>>>>>>>> looking at the system this appears to be the way it should be > >>>>>>>>>> assembled). > >>>>>>>>>> > >>>>>>>>>> I'll have to think about the best way to address this. In the > >>>>>>>>>> meantime, here is a potential workaround. You could unwrap the > >>>> entire > >>>>>>>>>> trajectory using the original input coordinates as a reference > >>>>>>>>>> (assuming the hexamer is "properly" formed there). You would > >> have > >>>> to > >>>>>>>>>> make certain you unwrap the trajectory in the right order, > >> i.e. in > >>>>>> the > >>>>>>>>>> same order it was simulated. You can then center on the hexamer > >>>> but > >>>>>>>>>> *only* image the water (and ions). So e.g. > >>>>>>>>>> > >>>>>>>>>> parm 1P9M_Hexamer.prmtop > >>>>>>>>>> reference pr90.rst7 > >>>>>>>>>> trajin run0.nc > >>>>>>>>>> trajin run1.nc > >>>>>>>>>> ... > >>>>>>>>>> unwrap reference > >>>>>>>>>> center :1-1330 > >>>>>>>>>> image :WAT,Na+ > >>>>>>>>>> > >>>>>>>>>> The idea is to keep the hexamer together by effectively never > >>>> imaging > >>>>>>>>>> it, then reimaging all the mobile stuff so it looks nice. I > >> think > >>>>>>>>>> (hope) this will work. > >>>>>>>>>> > >>>>>>>>>> Thanks for the files! > >>>>>>>>>> > >>>>>>>>>> -Dan > >>>>>>>>>> > >>>>>>>>>> On Mon, Jul 10, 2017 at 1:05 PM, Guqin Shi <shi.293.osu.edu> > >>>> wrote: > >>>>>>>>>>> Hi Dan, > >>>>>>>>>>> > >>>>>>>>>>> In addition to visualize trajectories pleasantly...my main > >>>> purpose > >>>>>> is > >>>>>>>> to > >>>>>>>>>>> get correct coordinates so that the following MMPBSA > >> calculation > >>>>>>>> could be > >>>>>>>>>>> carried out... (or maybe MMPBSA doesn't care about that at > >>>>>> all...??? > >>>>>>>>>> then I > >>>>>>>>>>> was wasting lots of my time...) > >>>>>>>>>>> > >>>>>>>>>>> I attached a prmtop with solvents stripped and a 1 ns of > >>>>>>>>>> nowat_coordinates > >>>>>>>>>>> (for the sake of file size) which I keep having problem > >> imaging > >>>>>> it... > >>>>>>>> ( > >>>>>>>>>>> https://drive.google.com/open?id= > >> 0B7kncIsWo85uSWJmbFBtczNtdFE) > >>>>>> Please > >>>>>>>>>> let > >>>>>>>>>>> me know if you feel solvated coordinates are needed... > >>>>>>>>>>> > >>>>>>>>>>> > >>>>>>>>>>> Thanks a lot!!! > >>>>>>>>>>> -Guqin > >>>>>>>>>>> > >>>>>>>>>>> On Mon, Jul 10, 2017 at 12:29 PM, Daniel Roe < > >>>>>> daniel.r.roe.gmail.com> > >>>>>>>>>> wrote: > >>>>>>>>>>>> Hi, > >>>>>>>>>>>> > >>>>>>>>>>>> (Could you send me some coordinates to go along with that > >>>> topology > >>>>>>>>>> file?) > >>>>>>>>>>>> On Mon, Jul 10, 2017 at 12:15 PM, Guqin Shi < > >> shi.293.osu.edu> > >>>>>> wrote: > >>>>>>>>>>>>> at the bottom edge of box......According to the original > >>>> prmtop > >>>>>>>> files, > >>>>>>>>>>>> the > >>>>>>>>>>>>> complex sits at the center of water box, but also > >> meantime, > >>>> it > >>>>>> sits > >>>>>>>>>> along > >>>>>>>>>>>>> the diagonal line...It seems center-image puts molecule > >> along > >>>>>> any > >>>>>>>> of > >>>>>>>>>> the > >>>>>>>>>>>>> side line and that's why it just couldn't fit all back...? > >>>> But I > >>>>>>>> am so > >>>>>>>>>>>>> confused now as why early trajectories could be imaged > >>>> without > >>>>>> any > >>>>>>>>>>>>> problem... > >>>>>>>>>>>> Re-imaging is more of an art than a science, mostly because > >>>>>> imaging > >>>>>>>> is > >>>>>>>>>>>> something that we do to make things "look nice". The > >> molecules > >>>>>> being > >>>>>>>>>>>> simulated don't care where they are absolutely, they only > >> care > >>>>>> where > >>>>>>>>>>>> they are with respect to other molecules. When you center on > >>>> one > >>>>>>>>>>>> molecule, you shift the coordinates of the entire system, > >> some > >>>> of > >>>>>>>>>>>> which move past the boundaries of your unit cell. Those > >> atoms > >>>> are > >>>>>>>> then > >>>>>>>>>>>> "wrapped" or re-imaged back inside the unit cell, which is > >> what > >>>>>> can > >>>>>>>>>>>> result in molecules appearing "separated". The 'autoimage' > >>>> command > >>>>>>>>>>>> tries to image in a way that keeps these molecules together > >> by > >>>>>>>>>>>> defining an anchor molecule/region (which is at the center), > >>>> and > >>>>>>>>>>>> molecules that are "fixed" to that anchor - it then tries to > >>>>>> minimize > >>>>>>>>>>>> the distance between the anchor and fixed molecules. Where > >> this > >>>>>> fails > >>>>>>>>>>>> is when a "wrapped" version of the system has shorter > >> distances > >>>>>> than > >>>>>>>>>>>> the "unwrapped version", which is typically because the > >>>>>> definition of > >>>>>>>>>>>> the anchor (center) is off. This is why the definition of > >> the > >>>>>>>> "anchor" > >>>>>>>>>>>> region is so crucial. > >>>>>>>>>>>> > >>>>>>>>>>>> Send me those coordinates and I'll see what can be done. > >>>>>>>>>>>> > >>>>>>>>>>>> -Dan > >>>>>>>>>>>> > >>>>>>>>>>>>> > >>>>>>>>>>>>> Thanks, > >>>>>>>>>>>>> Guqin > >>>>>>>>>>>>> > >>>>>>>>>>>>> On Mon, Jul 10, 2017 at 11:43 AM, Guqin Shi < > >>>> gshi.cop.ufl.edu> > >>>>>>>> wrote: > >>>>>>>>>>>>>> On Mon, Jul 10, 2017 at 8:32 AM, Daniel Roe < > >>>>>>>> daniel.r.roe.gmail.com> > >>>>>>>>>>>>>> wrote: > >>>>>>>>>>>>>> > >>>>>>>>>>>>>>> Hi, > >>>>>>>>>>>>>>> > >>>>>>>>>>>>>>> The key for 'autoimage' is that you need to specify a > >>>> region > >>>>>>>>>>>>>>> (molecule, residue, atom, etc) that visually you want to > >>>> be at > >>>>>>>> the > >>>>>>>>>>>>>>> center of your unit cell; in cpptraj this is called the > >>>>>>>> 'anchor'. By > >>>>>>>>>>>>>>> default 'autoimage' tries to use the first molecule to > >> do > >>>>>> this. > >>>>>>>>>>>>>>> However in certain systems another choice is better. For > >>>>>>>> example, if > >>>>>>>>>>>>>>> you have a dimer then you would want to choose 1 or more > >>>>>> residues > >>>>>>>>>> that > >>>>>>>>>>>>>>> are near the center of the interface between the two > >>>> monomers > >>>>>> as > >>>>>>>>>> your > >>>>>>>>>>>>>>> anchor. Without seeing your system I can't make specific > >>>>>>>>>>>>>>> recommendations, but you could try experimenting with > >>>>>> different > >>>>>>>>>> anchor > >>>>>>>>>>>>>>> points. If you'd like, send me a PDB file or > >>>> topology/restart > >>>>>>>> files > >>>>>>>>>> of > >>>>>>>>>>>>>>> your system off-list and I can try to recommend an > >> anchor. > >>>>>>>>>>>>>>> -Dan > >>>>>>>>>>>>>>> > >>>>>>>>>>>>>>> > >>>>>>>>>>>>>> Hi Bill, > >>>>>>>>>>>>>> > >>>>>>>>>>>>>> Thanks for pointing out the key point of "autoimage". I > >>>> tried > >>>>>> to > >>>>>>>> play > >>>>>>>>>>>> with > >>>>>>>>>>>>>> autoimage-anchor a little bit by myself. I noticed that > >> the > >>>>>> mask > >>>>>>>> for > >>>>>>>>>>>>>> autoimage are molecule-wise, instead of residue-wise... > >>>>>> Therefore > >>>>>>>>>> when I > >>>>>>>>>>>>>> specify some center residues, cpptraj reports back with > >>>> error > >>>>>>>> (Error: > >>>>>>>>>>>>>> Anchor mask [:153-155] corresponds to 0 mols, should > >> only be > >>>>>> 1.) > >>>>>>>> and > >>>>>>>>>>>> then > >>>>>>>>>>>>>> it goes with default again... Maybe my syntax is somehow > >> not > >>>>>>>> correct? > >>>>>>>>>>>>>> Also, my system is a little bit special. It is a "dimer" > >> and > >>>>>> each > >>>>>>>>>>>> monomer > >>>>>>>>>>>>>> contains three molecules. There is a hollow in between > >> the > >>>> two > >>>>>>>>>> dimers... > >>>>>>>>>>>>>> Currently in my own practice, I picked three residues on > >>>> each > >>>>>> of > >>>>>>>> the > >>>>>>>>>>>> dimer > >>>>>>>>>>>>>> which I think, are the closest to the center of cell > >>>> (143-155 & > >>>>>>>>>>>> 818-820). > >>>>>>>>>>>>>> Also, since these residues are symmetric, I am not sure > >> how > >>>> the > >>>>>>>>>> program > >>>>>>>>>>>>>> would place them in terms of direction...or maybe in this > >>>> case, > >>>>>>>>>>>> asymmetric > >>>>>>>>>>>>>> residues might be better...? I attached the prmtop file > >>>> (with > >>>>>>>>>>>> solvens/ions) > >>>>>>>>>>>>>> here on my google drive: > >>>>>>>>>>>>>> https://drive.google.com/open?id= > >>>> 0B7kncIsWo85ud1BweGJfd1h1ZXM > >>>>>>>>>> (Since it > >>>>>>>>>>>>>> is quite big so I don't think mailing list server would > >>>> allow > >>>>>> that > >>>>>>>>>>>> size..) > >>>>>>>>>>>>>> Could you also check my system to see if my choice on > >>>> residues > >>>>>> are > >>>>>>>>>> good > >>>>>>>>>>>> or > >>>>>>>>>>>>>> maybe another set of residues are better..? > >>>>>>>>>>>>>> > >>>>>>>>>>>>>> > >>>>>>>>>>>>>> Thanks a lot for your help! > >>>>>>>>>>>>>> -Guqin > >>>>>>>>>>>>>> > >>>>>>>>>>>>>> -- > >>>>>>>>>>>>>> Guqin SHI > >>>>>>>>>>>>>> 1345 Center Drive > >>>>>>>>>>>>>> College of Pharmacy > >>>>>>>>>>>>>> PO Box 100485 > >>>>>>>>>>>>>> University of Florida > >>>>>>>>>>>>>> Gainesville, FL 32610 > >>>>>>>>>>>>>> > >>>>>>>>>>>>> > >>>>>>>>>>>>> > >>>>>>>>>>>>> -- > >>>>>>>>>>>>> Guqin SHI > >>>>>>>>>>>>> PhD Candidate in Medicinal Chemistry and Pharmacognosy > >>>>>>>>>>>>> College of Pharmacy > >>>>>>>>>>>>> The Ohio State University > >>>>>>>>>>>>> Columbus, OH, 43210 > >>>>>>>>>>>>> _______________________________________________ > >>>>>>>>>>>>> AMBER mailing list > >>>>>>>>>>>>> AMBER.ambermd.org > >>>>>>>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber > >>>>>>>>>>>> > >>>>>>>>>>>> > >>>>>>>>>>>> -- > >>>>>>>>>>>> ------------------------- > >>>>>>>>>>>> Daniel R. Roe > >>>>>>>>>>>> Laboratory of Computational Biology > >>>>>>>>>>>> National Institutes of Health, NHLBI > >>>>>>>>>>>> 5635 Fishers Ln, Rm T900 > >>>>>>>>>>>> Rockville MD, 20852 > >>>>>>>>>>>> https://www.lobos.nih.gov/lcb > >>>>>>>>>>>> > >>>>>>>>>>>> _______________________________________________ > >>>>>>>>>>>> AMBER mailing list > >>>>>>>>>>>> AMBER.ambermd.org > >>>>>>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber > >>>>>>>>>>>> > >>>>>>>>>>> > >>>>>>>>>>> > >>>>>>>>>>> -- > >>>>>>>>>>> Guqin SHI > >>>>>>>>>>> PhD Candidate in Medicinal Chemistry and Pharmacognosy > >>>>>>>>>>> College of Pharmacy > >>>>>>>>>>> The Ohio State University > >>>>>>>>>>> Columbus, OH, 43210 > >>>>>>>>>>> _______________________________________________ > >>>>>>>>>>> AMBER mailing list > >>>>>>>>>>> AMBER.ambermd.org > >>>>>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber > >>>>>>>>>> > >>>>>>>>>> > >>>>>>>>>> -- > >>>>>>>>>> ------------------------- > >>>>>>>>>> Daniel R. Roe > >>>>>>>>>> Laboratory of Computational Biology > >>>>>>>>>> National Institutes of Health, NHLBI > >>>>>>>>>> 5635 Fishers Ln, Rm T900 > >>>>>>>>>> Rockville MD, 20852 > >>>>>>>>>> https://www.lobos.nih.gov/lcb > >>>>>>>>>> > >>>>>>>>>> _______________________________________________ > >>>>>>>>>> AMBER mailing list > >>>>>>>>>> AMBER.ambermd.org > >>>>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber > >>>>>>>>>> > >>>>>>>>> > >>>>>>>>> > >>>>>>>>> -- > >>>>>>>>> Guqin SHI > >>>>>>>>> PhD Candidate in Medicinal Chemistry and Pharmacognosy > >>>>>>>>> College of Pharmacy > >>>>>>>>> The Ohio State University > >>>>>>>>> Columbus, OH, 43210 > >>>>>>>>> _______________________________________________ > >>>>>>>>> AMBER mailing list > >>>>>>>>> AMBER.ambermd.org > >>>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber > >>>>>>>> > >>>>>>>> > >>>>>>>> -- > >>>>>>>> ------------------------- > >>>>>>>> Daniel R. Roe > >>>>>>>> Laboratory of Computational Biology > >>>>>>>> National Institutes of Health, NHLBI > >>>>>>>> 5635 Fishers Ln, Rm T900 > >>>>>>>> Rockville MD, 20852 > >>>>>>>> https://www.lobos.nih.gov/lcb > >>>>>>>> > >>>>>>>> _______________________________________________ > >>>>>>>> AMBER mailing list > >>>>>>>> AMBER.ambermd.org > >>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber > >>>>>>>> > >>>>>>> > >>>>>>> > >>>>>>> -- > >>>>>>> Guqin SHI > >>>>>>> PhD Candidate in Medicinal Chemistry and Pharmacognosy > >>>>>>> College of Pharmacy > >>>>>>> The Ohio State University > >>>>>>> Columbus, OH, 43210 > >>>>>>> _______________________________________________ > >>>>>>> AMBER mailing list > >>>>>>> AMBER.ambermd.org > >>>>>>> http://lists.ambermd.org/mailman/listinfo/amber > >>>>>> > >>>>>> > >>>>>> -- > >>>>>> ------------------------- > >>>>>> Daniel R. Roe > >>>>>> Laboratory of Computational Biology > >>>>>> National Institutes of Health, NHLBI > >>>>>> 5635 Fishers Ln, Rm T900 > >>>>>> Rockville MD, 20852 > >>>>>> https://www.lobos.nih.gov/lcb > >>>>>> > >>>>>> _______________________________________________ > >>>>>> AMBER mailing list > >>>>>> AMBER.ambermd.org > >>>>>> http://lists.ambermd.org/mailman/listinfo/amber > >>>>>> > >>>>> > >>>>> > >>>>> -- > >>>>> Guqin SHI > >>>>> PhD Candidate in Medicinal Chemistry and Pharmacognosy > >>>>> College of Pharmacy > >>>>> The Ohio State University > >>>>> Columbus, OH, 43210 > >>>>> _______________________________________________ > >>>>> AMBER mailing list > >>>>> AMBER.ambermd.org > >>>>> http://lists.ambermd.org/mailman/listinfo/amber > >>>> > >>>> > >>>> -- > >>>> ------------------------- > >>>> Daniel R. Roe > >>>> Laboratory of Computational Biology > >>>> National Institutes of Health, NHLBI > >>>> 5635 Fishers Ln, Rm T900 > >>>> Rockville MD, 20852 > >>>> https://www.lobos.nih.gov/lcb > >>>> > >>>> _______________________________________________ > >>>> AMBER mailing list > >>>> AMBER.ambermd.org > >>>> http://lists.ambermd.org/mailman/listinfo/amber > >>>> > >>> > >>> > >>> -- > >>> Guqin SHI > >>> PhD Candidate in Medicinal Chemistry and Pharmacognosy > >>> College of Pharmacy > >>> The Ohio State University > >>> Columbus, OH, 43210 > >>> > >>> _______________________________________________ > >>> AMBER mailing list > >>> AMBER.ambermd.org > >>> http://lists.ambermd.org/mailman/listinfo/amber > >>> > >> > >> > >> -- > >> ------------------------- > >> Daniel R. Roe > >> Laboratory of Computational Biology > >> National Institutes of Health, NHLBI > >> 5635 Fishers Ln, Rm T900 > >> Rockville MD, 20852 > >> https://www.lobos.nih.gov/lcb > >> > >> _______________________________________________ > >> AMBER mailing list > >> AMBER.ambermd.org > >> http://lists.ambermd.org/mailman/listinfo/amber > >> > > > > > > > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber > -- Guqin SHI PhD Candidate in Medicinal Chemistry and Pharmacognosy College of Pharmacy The Ohio State University Columbus, OH, 43210 ------------------------------ Message: 8 Date: Wed, 12 Jul 2017 15:07:02 -0700 From: Bill Ross <ross.cgl.ucsf.edu> Subject: Re: [AMBER] Suggestions about Center and Image for multiple-molecule complex To: amber.ambermd.org Message-ID: <ba1e62ee-9577-daf9-4294-faf0f54f0f32.cgl.ucsf.edu> Content-Type: text/plain; charset=utf-8; format=flowed Hi Guqin, > But I don't know for this method, how general it could be and > how efficient it will be (considering the translation have to be done on > all axes and iterations will be done on all mols/atoms...) I have no > experience or idea. But I would love to follow up with updates if future >cpptraj would have such changes. I don't know about python speed for such tasks. Likely optimizations are possible. E.g. that inner 'if' I mentioned shouldn't be necessary, and maybe something could be done with centroids of molecules. And one would only calc inter-molecular distances, not the intra's since they would be constant. It's just a suggestion on my part, since I'm not working in the field. Regards, Bill On 7/12/17 2:54 PM, Guqin Shi wrote: > Hi Bill, > > Thanks for your suggestion on this problem. Dan helped add a new option and > seemingly solved the problem. (I am writing this email and saw your new > reply just came in.) > > But I did go to check the "pytraj" and I am glad I did so. Previously I > used cpptraj to get results and write separate python script to process or > plot the data; but with pytraj it seems two steps could be merged into one. > Although I didn't utilize pytraj to solve this problem but it's good to > know it. > > As for your previous suggestion on image minimizer, I kinda get your idea. > Because while Dan was developing the new option, I was using topotools in > vmd to write protein coordinates from adjacent cells and picked out an > intact hexamer manually. This is basically (from my understanding...) what > you were mentioning: get translated images/coordinates and the molecules > with the closest distance should theoretically be in the "correct" > complex... But I don't know for this method, how general it could be and > how efficient it will be (considering the translation have to be done on > all axes and iterations will be done on all mols/atoms...) I have no > experience or idea. But I would love to follow up with updates if future > cpptraj would have such changes. > > Best, > Guqin > > On Wed, Jul 12, 2017 at 5:37 PM, Bill Ross <ross.cgl.ucsf.edu> wrote: > >> I still wonder if my idea would be a more general solution, requiring no >> thought on the user's part. >> >> Bill >> >> >> On 7/12/17 2:34 PM, Guqin Shi wrote: >>> Hi Dan, >>> >>> I want to let you know that I have tested the new option for my latest >>> trajectories. It works very well so far. >>> The default "autoimage" worked well until 86 ns that conventional way >>> couldn't work anymore in my case. Then "autoimage" with "moveanchor" were >>> performed on the following trajectories and so far so good. However, my >>> simulation is still ongoing. So I will keep testing and report back until >>> my simulation is done. >>> >>> As to the cpptraj tests, "make check" showed that all tests are passed. >> So >>> at least nothing I need to worry for now... >>> >>> >>> Thanks a lot for your time and help! I am glad that my special system >> help >>> raise a new option... >>> >>> Best, >>> Guqin >>> >>> On Wed, Jul 12, 2017 at 10:39 AM, Daniel Roe <daniel.r.roe.gmail.com> >> wrote: >>>> Hi, >>>> >>>> On Wed, Jul 12, 2017 at 10:32 AM, Guqin Shi <shi.293.osu.edu> wrote: >>>>> I have multiple production run trajectories which have similar >> problems. >>>> I >>>>> will test them one by one to see how things going. It might take a >>>> while. I >>>>> will report back hopefully by tomorrow. >>>> Great - all feedback is appreciated! >>>> >>>>> When I installed cpptraj, there were some warnings. One of them is >>>>> "Compilation with Sander API failed: (during ./configure). Others are >>>> This is because your Amber installation is from Amber 14 and the >>>> sander API has changed since then. Cpptraj's configure detects this >>>> and disables the sander interface accordingly. >>>> >>>>> function warnings such as "unused variable" or "uninitialized" (during >>>>> "make install"). I attached a file containing these warning messages. I >>>> These warnings have to do with the 'readline' and 'xdr' libraries and >>>> can be safely ignored. The real check is to 'make check' in >>>> $CPPTRAJHOME or 'make test.all' in $CPPTRAJHOME/test. >>>> >>>> Hope this helps, >>>> >>>> -Dan >>>> >>>>> think the latter should be ok. As to the failure with sander API, is >> this >>>>> something I need to worry about considering future usage...? >>>>> >>>>> >>>>> Thanks a lot for the help! Great start for today's work!! >>>>> -Guqin >>>>> >>>>> On Wed, Jul 12, 2017 at 10:03 AM, Daniel Roe <daniel.r.roe.gmail.com> >>>> wrote: >>>>>> On Wed, Jul 12, 2017 at 9:55 AM, Guqin Shi <shi.293.osu.edu> wrote: >>>>>>> Or maybe I can replace these two files under my current >>>>>>> $AMBERHOME/AmberTools/src/cpptraj/src directory..? >>>>>> This may not work. The GitHub version of cpptraj tends to diverge from >>>>>> the AmberTools release pretty quickly. This can also mess up future >>>>>> AmberTools updates. Just stick with the separate install for now. >>>>>> >>>>>> -Dan >>>>>> >>>>>>> Thanks, >>>>>>> Guqin >>>>>>> >>>>>>> On Wed, Jul 12, 2017 at 8:07 AM, Daniel Roe <daniel.r.roe.gmail.com> >>>>>> wrote: >>>>>>>> Hi, >>>>>>>> >>>>>>>> The new option is live: https://github.com/Amber-MD/ >> cpptraj/pull/515 >>>>>>>> Just try adding the 'moveanchor' option to your 'autoimage' command. >>>>>>>> It worked for the frames that you sent me. What it does is that when >>>>>>>> imaging 'fixed' molecules it uses the previous molecule as the >> anchor >>>>>>>> point (the first fixed molecule uses the original anchor point). >> This >>>>>>>> probably will only work when molecules are both close in sequence >> and >>>>>>>> geometrically close. >>>>>>>> >>>>>>>> Try it and let me know if it works. >>>>>>>> >>>>>>>> -Dan >>>>>>>> >>>>>>>> On Tue, Jul 11, 2017 at 4:35 PM, Guqin Shi <shi.293.osu.edu> wrote: >>>>>>>>> Oh my god...it just made my day... >>>>>>>>> I've been desperately looking for solutions today... for example, >>>> I am >>>>>>>>> currently using the topotools plugged in VMD to write coordinates >>>> of >>>>>>>>> replicates from adjacent cells and trying to pick out the >>>> coordinates >>>>>> of >>>>>>>> an >>>>>>>>> intact complex...meantime I am worrying about the precision, the >>>>>>>> potential >>>>>>>>> artifacts, and speeds in processing massive of frames... >>>>>>>>> >>>>>>>>> -Guqin >>>>>>>>> >>>>>>>>> On Tue, Jul 11, 2017 at 3:52 PM, Daniel Roe < >>>> daniel.r.roe.gmail.com> >>>>>>>> wrote: >>>>>>>>>> I think I have a fix (really a new autoimage option) that seems to >>>>>>>>>> work. I'm testing now and will let you know when it's live. >>>>>>>>>> >>>>>>>>>> -Dan >>>>>>>>>> >>>>>>>>>> On Tue, Jul 11, 2017 at 11:46 AM, Guqin Shi <shi.293.osu.edu> >>>> wrote: >>>>>>>>>>> Hi Dan, >>>>>>>>>>> >>>>>>>>>>> this is really unfortunate but the unwrap doesn't work either... >>>>>> The >>>>>>>>>>> resulting coordinates are similar to autoimage/center-image that >>>>>> one >>>>>>>> of >>>>>>>>>> the >>>>>>>>>>> molecules is still left outside... >>>>>>>>>>> In the Amber manual, there is a notation that "this command >>>> fails >>>>>> when >>>>>>>>>> the >>>>>>>>>>> masked molecules travel more than half of the box size within a >>>>>> single >>>>>>>>>>> frame." Is this the reason that unwrap couldn't work either...? >>>>>>>>>>> >>>>>>>>>>> I uploaded the raw coordinates of pr90 and the original input >>>>>>>> coordinates >>>>>>>>>>> pdb file into the folder. I also uploaded the an >>>>>> test_unwrap_copy.in >>>>>>>>>> file >>>>>>>>>>> which contains the commands I used for reference-unwrap... I >>>>>> comment >>>>>>>> out >>>>>>>>>>> center and image commands as since the unwrap failed, center and >>>>>> image >>>>>>>>>>> won't help much.. >>>>>>>>>>> >>>>>>>>>>> If you have time, would you mind having a look at >>>> them...Thanks... >>>>>>>>>>> Best, >>>>>>>>>>> Guqin >>>>>>>>>>> >>>>>>>>>>> On Tue, Jul 11, 2017 at 9:00 AM, Daniel Roe < >>>>>> daniel.r.roe.gmail.com> >>>>>>>>>> wrote: >>>>>>>>>>>> Wow - this is certainly a challenging system to image! No one >>>>>>>> molecule >>>>>>>>>>>> can be considered "center" - in fact, there isn't even a region >>>>>> of a >>>>>>>>>>>> molecule that can be considered to be the center since when the >>>>>>>>>>>> hexamer is formed there is a large empty space in the center >>>> (from >>>>>>>>>>>> looking at the system this appears to be the way it should be >>>>>>>>>>>> assembled). >>>>>>>>>>>> >>>>>>>>>>>> I'll have to think about the best way to address this. In the >>>>>>>>>>>> meantime, here is a potential workaround. You could unwrap the >>>>>> entire >>>>>>>>>>>> trajectory using the original input coordinates as a reference >>>>>>>>>>>> (assuming the hexamer is "properly" formed there). You would >>>> have >>>>>> to >>>>>>>>>>>> make certain you unwrap the trajectory in the right order, >>>> i.e. in >>>>>>>> the >>>>>>>>>>>> same order it was simulated. You can then center on the hexamer >>>>>> but >>>>>>>>>>>> *only* image the water (and ions). So e.g. >>>>>>>>>>>> >>>>>>>>>>>> parm 1P9M_Hexamer.prmtop >>>>>>>>>>>> reference pr90.rst7 >>>>>>>>>>>> trajin run0.nc >>>>>>>>>>>> trajin run1.nc >>>>>>>>>>>> ... >>>>>>>>>>>> unwrap reference >>>>>>>>>>>> center :1-1330 >>>>>>>>>>>> image :WAT,Na+ >>>>>>>>>>>> >>>>>>>>>>>> The idea is to keep the hexamer together by effectively never >>>>>> imaging >>>>>>>>>>>> it, then reimaging all the mobile stuff so it looks nice. I >>>> think >>>>>>>>>>>> (hope) this will work. >>>>>>>>>>>> >>>>>>>>>>>> Thanks for the files! >>>>>>>>>>>> >>>>>>>>>>>> -Dan >>>>>>>>>>>> >>>>>>>>>>>> On Mon, Jul 10, 2017 at 1:05 PM, Guqin Shi <shi.293.osu.edu> >>>>>> wrote: >>>>>>>>>>>>> Hi Dan, >>>>>>>>>>>>> >>>>>>>>>>>>> In addition to visualize trajectories pleasantly...my main >>>>>> purpose >>>>>>>> is >>>>>>>>>> to >>>>>>>>>>>>> get correct coordinates so that the following MMPBSA >>>> calculation >>>>>>>>>> could be >>>>>>>>>>>>> carried out... (or maybe MMPBSA doesn't care about that at >>>>>>>> all...??? >>>>>>>>>>>> then I >>>>>>>>>>>>> was wasting lots of my time...) >>>>>>>>>>>>> >>>>>>>>>>>>> I attached a prmtop with solvents stripped and a 1 ns of >>>>>>>>>>>> nowat_coordinates >>>>>>>>>>>>> (for the sake of file size) which I keep having problem >>>> imaging >>>>>>>> it... >>>>>>>>>> ( >>>>>>>>>>>>> https://drive.google.com/open?id= >>>> 0B7kncIsWo85uSWJmbFBtczNtdFE) >>>>>>>> Please >>>>>>>>>>>> let >>>>>>>>>>>>> me know if you feel solvated coordinates are needed... >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> Thanks a lot!!! >>>>>>>>>>>>> -Guqin >>>>>>>>>>>>> >>>>>>>>>>>>> On Mon, Jul 10, 2017 at 12:29 PM, Daniel Roe < >>>>>>>> daniel.r.roe.gmail.com> >>>>>>>>>>>> wrote: >>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>> >>>>>>>>>>>>>> (Could you send me some coordinates to go along with that >>>>>> topology >>>>>>>>>>>> file?) >>>>>>>>>>>>>> On Mon, Jul 10, 2017 at 12:15 PM, Guqin Shi < >>>> shi.293.osu.edu> >>>>>>>> wrote: >>>>>>>>>>>>>>> at the bottom edge of box......According to the original >>>>>> prmtop >>>>>>>>>> files, >>>>>>>>>>>>>> the >>>>>>>>>>>>>>> complex sits at the center of water box, but also >>>> meantime, >>>>>> it >>>>>>>> sits >>>>>>>>>>>> along >>>>>>>>>>>>>>> the diagonal line...It seems center-image puts molecule >>>> along >>>>>>>> any >>>>>>>>>> of >>>>>>>>>>>> the >>>>>>>>>>>>>>> side line and that's why it just couldn't fit all back...? >>>>>> But I >>>>>>>>>> am so >>>>>>>>>>>>>>> confused now as why early trajectories could be imaged >>>>>> without >>>>>>>> any >>>>>>>>>>>>>>> problem... >>>>>>>>>>>>>> Re-imaging is more of an art than a science, mostly because >>>>>>>> imaging >>>>>>>>>> is >>>>>>>>>>>>>> something that we do to make things "look nice". The >>>> molecules >>>>>>>> being >>>>>>>>>>>>>> simulated don't care where they are absolutely, they only >>>> care >>>>>>>> where >>>>>>>>>>>>>> they are with respect to other molecules. When you center on >>>>>> one >>>>>>>>>>>>>> molecule, you shift the coordinates of the entire system, >>>> some >>>>>> of >>>>>>>>>>>>>> which move past the boundaries of your unit cell. Those >>>> atoms >>>>>> are >>>>>>>>>> then >>>>>>>>>>>>>> "wrapped" or re-imaged back inside the unit cell, which is >>>> what >>>>>>>> can >>>>>>>>>>>>>> result in molecules appearing "separated". The 'autoimage' >>>>>> command >>>>>>>>>>>>>> tries to image in a way that keeps these molecules together >>>> by >>>>>>>>>>>>>> defining an anchor molecule/region (which is at the center), >>>>>> and >>>>>>>>>>>>>> molecules that are "fixed" to that anchor - it then tries to >>>>>>>> minimize >>>>>>>>>>>>>> the distance between the anchor and fixed molecules. Where >>>> this >>>>>>>> fails >>>>>>>>>>>>>> is when a "wrapped" version of the system has shorter >>>> distances >>>>>>>> than >>>>>>>>>>>>>> the "unwrapped version", which is typically because the >>>>>>>> definition of >>>>>>>>>>>>>> the anchor (center) is off. This is why the definition of >>>> the >>>>>>>>>> "anchor" >>>>>>>>>>>>>> region is so crucial. >>>>>>>>>>>>>> >>>>>>>>>>>>>> Send me those coordinates and I'll see what can be done. >>>>>>>>>>>>>> >>>>>>>>>>>>>> -Dan >>>>>>>>>>>>>> >>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>> Guqin >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> On Mon, Jul 10, 2017 at 11:43 AM, Guqin Shi < >>>>>> gshi.cop.ufl.edu> >>>>>>>>>> wrote: >>>>>>>>>>>>>>>> On Mon, Jul 10, 2017 at 8:32 AM, Daniel Roe < >>>>>>>>>> daniel.r.roe.gmail.com> >>>>>>>>>>>>>>>> wrote: >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> The key for 'autoimage' is that you need to specify a >>>>>> region >>>>>>>>>>>>>>>>> (molecule, residue, atom, etc) that visually you want to >>>>>> be at >>>>>>>>>> the >>>>>>>>>>>>>>>>> center of your unit cell; in cpptraj this is called the >>>>>>>>>> 'anchor'. By >>>>>>>>>>>>>>>>> default 'autoimage' tries to use the first molecule to >>>> do >>>>>>>> this. >>>>>>>>>>>>>>>>> However in certain systems another choice is better. For >>>>>>>>>> example, if >>>>>>>>>>>>>>>>> you have a dimer then you would want to choose 1 or more >>>>>>>> residues >>>>>>>>>>>> that >>>>>>>>>>>>>>>>> are near the center of the interface between the two >>>>>> monomers >>>>>>>> as >>>>>>>>>>>> your >>>>>>>>>>>>>>>>> anchor. Without seeing your system I can't make specific >>>>>>>>>>>>>>>>> recommendations, but you could try experimenting with >>>>>>>> different >>>>>>>>>>>> anchor >>>>>>>>>>>>>>>>> points. If you'd like, send me a PDB file or >>>>>> topology/restart >>>>>>>>>> files >>>>>>>>>>>> of >>>>>>>>>>>>>>>>> your system off-list and I can try to recommend an >>>> anchor. >>>>>>>>>>>>>>>>> -Dan >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Hi Bill, >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Thanks for pointing out the key point of "autoimage". I >>>>>> tried >>>>>>>> to >>>>>>>>>> play >>>>>>>>>>>>>> with >>>>>>>>>>>>>>>> autoimage-anchor a little bit by myself. I noticed that >>>> the >>>>>>>> mask >>>>>>>>>> for >>>>>>>>>>>>>>>> autoimage are molecule-wise, instead of residue-wise... >>>>>>>> Therefore >>>>>>>>>>>> when I >>>>>>>>>>>>>>>> specify some center residues, cpptraj reports back with >>>>>> error >>>>>>>>>> (Error: >>>>>>>>>>>>>>>> Anchor mask [:153-155] corresponds to 0 mols, should >>>> only be >>>>>>>> 1.) >>>>>>>>>> and >>>>>>>>>>>>>> then >>>>>>>>>>>>>>>> it goes with default again... Maybe my syntax is somehow >>>> not >>>>>>>>>> correct? >>>>>>>>>>>>>>>> Also, my system is a little bit special. It is a "dimer" >>>> and >>>>>>>> each >>>>>>>>>>>>>> monomer >>>>>>>>>>>>>>>> contains three molecules. There is a hollow in between >>>> the >>>>>> two >>>>>>>>>>>> dimers... >>>>>>>>>>>>>>>> Currently in my own practice, I picked three residues on >>>>>> each >>>>>>>> of >>>>>>>>>> the >>>>>>>>>>>>>> dimer >>>>>>>>>>>>>>>> which I think, are the closest to the center of cell >>>>>> (143-155 & >>>>>>>>>>>>>> 818-820). >>>>>>>>>>>>>>>> Also, since these residues are symmetric, I am not sure >>>> how >>>>>> the >>>>>>>>>>>> program >>>>>>>>>>>>>>>> would place them in terms of direction...or maybe in this >>>>>> case, >>>>>>>>>>>>>> asymmetric >>>>>>>>>>>>>>>> residues might be better...? I attached the prmtop file >>>>>> (with >>>>>>>>>>>>>> solvens/ions) >>>>>>>>>>>>>>>> here on my google drive: >>>>>>>>>>>>>>>> https://drive.google.com/open?id= >>>>>> 0B7kncIsWo85ud1BweGJfd1h1ZXM >>>>>>>>>>>> (Since it >>>>>>>>>>>>>>>> is quite big so I don't think mailing list server would >>>>>> allow >>>>>>>> that >>>>>>>>>>>>>> size..) >>>>>>>>>>>>>>>> Could you also check my system to see if my choice on >>>>>> residues >>>>>>>> are >>>>>>>>>>>> good >>>>>>>>>>>>>> or >>>>>>>>>>>>>>>> maybe another set of residues are better..? >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Thanks a lot for your help! >>>>>>>>>>>>>>>> -Guqin >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>> Guqin SHI >>>>>>>>>>>>>>>> 1345 Center Drive >>>>>>>>>>>>>>>> College of Pharmacy >>>>>>>>>>>>>>>> PO Box 100485 >>>>>>>>>>>>>>>> University of Florida >>>>>>>>>>>>>>>> Gainesville, FL 32610 >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>> Guqin SHI >>>>>>>>>>>>>>> PhD Candidate in Medicinal Chemistry and Pharmacognosy >>>>>>>>>>>>>>> College of Pharmacy >>>>>>>>>>>>>>> The Ohio State University >>>>>>>>>>>>>>> Columbus, OH, 43210 >>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>> AMBER mailing list >>>>>>>>>>>>>>> AMBER.ambermd.org >>>>>>>>>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber >>>>>>>>>>>>>> >>>>>>>>>>>>>> -- >>>>>>>>>>>>>> ------------------------- >>>>>>>>>>>>>> Daniel R. Roe >>>>>>>>>>>>>> Laboratory of Computational Biology >>>>>>>>>>>>>> National Institutes of Health, NHLBI >>>>>>>>>>>>>> 5635 Fishers Ln, Rm T900 >>>>>>>>>>>>>> Rockville MD, 20852 >>>>>>>>>>>>>> https://www.lobos.nih.gov/lcb >>>>>>>>>>>>>> >>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>> AMBER mailing list >>>>>>>>>>>>>> AMBER.ambermd.org >>>>>>>>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber >>>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> -- >>>>>>>>>>>>> Guqin SHI >>>>>>>>>>>>> PhD Candidate in Medicinal Chemistry and Pharmacognosy >>>>>>>>>>>>> College of Pharmacy >>>>>>>>>>>>> The Ohio State University >>>>>>>>>>>>> Columbus, OH, 43210 >>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>> AMBER mailing list >>>>>>>>>>>>> AMBER.ambermd.org >>>>>>>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber >>>>>>>>>>>> >>>>>>>>>>>> -- >>>>>>>>>>>> ------------------------- >>>>>>>>>>>> Daniel R. Roe >>>>>>>>>>>> Laboratory of Computational Biology >>>>>>>>>>>> National Institutes of Health, NHLBI >>>>>>>>>>>> 5635 Fishers Ln, Rm T900 >>>>>>>>>>>> Rockville MD, 20852 >>>>>>>>>>>> https://www.lobos.nih.gov/lcb >>>>>>>>>>>> >>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>> AMBER mailing list >>>>>>>>>>>> AMBER.ambermd.org >>>>>>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber >>>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> -- >>>>>>>>>>> Guqin SHI >>>>>>>>>>> PhD Candidate in Medicinal Chemistry and Pharmacognosy >>>>>>>>>>> College of Pharmacy >>>>>>>>>>> The Ohio State University >>>>>>>>>>> Columbus, OH, 43210 >>>>>>>>>>> _______________________________________________ >>>>>>>>>>> AMBER mailing list >>>>>>>>>>> AMBER.ambermd.org >>>>>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber >>>>>>>>>> >>>>>>>>>> -- >>>>>>>>>> ------------------------- >>>>>>>>>> Daniel R. Roe >>>>>>>>>> Laboratory of Computational Biology >>>>>>>>>> National Institutes of Health, NHLBI >>>>>>>>>> 5635 Fishers Ln, Rm T900 >>>>>>>>>> Rockville MD, 20852 >>>>>>>>>> https://www.lobos.nih.gov/lcb >>>>>>>>>> >>>>>>>>>> _______________________________________________ >>>>>>>>>> AMBER mailing list >>>>>>>>>> AMBER.ambermd.org >>>>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber >>>>>>>>>> >>>>>>>>> >>>>>>>>> -- >>>>>>>>> Guqin SHI >>>>>>>>> PhD Candidate in Medicinal Chemistry and Pharmacognosy >>>>>>>>> College of Pharmacy >>>>>>>>> The Ohio State University >>>>>>>>> Columbus, OH, 43210 >>>>>>>>> _______________________________________________ >>>>>>>>> AMBER mailing list >>>>>>>>> AMBER.ambermd.org >>>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber >>>>>>>> >>>>>>>> -- >>>>>>>> ------------------------- >>>>>>>> Daniel R. Roe >>>>>>>> Laboratory of Computational Biology >>>>>>>> National Institutes of Health, NHLBI >>>>>>>> 5635 Fishers Ln, Rm T900 >>>>>>>> Rockville MD, 20852 >>>>>>>> https://www.lobos.nih.gov/lcb >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> AMBER mailing list >>>>>>>> AMBER.ambermd.org >>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber >>>>>>>> >>>>>>> >>>>>>> -- >>>>>>> Guqin SHI >>>>>>> PhD Candidate in Medicinal Chemistry and Pharmacognosy >>>>>>> College of Pharmacy >>>>>>> The Ohio State University >>>>>>> Columbus, OH, 43210 >>>>>>> _______________________________________________ >>>>>>> AMBER mailing list >>>>>>> AMBER.ambermd.org >>>>>>> http://lists.ambermd.org/mailman/listinfo/amber >>>>>> >>>>>> -- >>>>>> ------------------------- >>>>>> Daniel R. Roe >>>>>> Laboratory of Computational Biology >>>>>> National Institutes of Health, NHLBI >>>>>> 5635 Fishers Ln, Rm T900 >>>>>> Rockville MD, 20852 >>>>>> https://www.lobos.nih.gov/lcb >>>>>> >>>>>> _______________________________________________ >>>>>> AMBER mailing list >>>>>> AMBER.ambermd.org >>>>>> http://lists.ambermd.org/mailman/listinfo/amber >>>>>> >>>>> >>>>> -- >>>>> Guqin SHI >>>>> PhD Candidate in Medicinal Chemistry and Pharmacognosy >>>>> College of Pharmacy >>>>> The Ohio State University >>>>> Columbus, OH, 43210 >>>>> >>>>> _______________________________________________ >>>>> AMBER mailing list >>>>> AMBER.ambermd.org >>>>> http://lists.ambermd.org/mailman/listinfo/amber >>>>> >>>> >>>> -- >>>> ------------------------- >>>> Daniel R. Roe >>>> Laboratory of Computational Biology >>>> National Institutes of Health, NHLBI >>>> 5635 Fishers Ln, Rm T900 >>>> Rockville MD, 20852 >>>> https://www.lobos.nih.gov/lcb >>>> >>>> _______________________________________________ >>>> AMBER mailing list >>>> AMBER.ambermd.org >>>> http://lists.ambermd.org/mailman/listinfo/amber >>>> >>> >> >> _______________________________________________ >> AMBER mailing list >> AMBER.ambermd.org >> http://lists.ambermd.org/mailman/listinfo/amber >> > > ------------------------------ Message: 9 Date: Wed, 12 Jul 2017 18:18:06 -0400 From: Hai Nguyen <nhai.qn.gmail.com> Subject: Re: [AMBER] Suggestions about Center and Image for multiple-molecule complex To: AMBER Mailing List <amber.ambermd.org> Message-ID: <CAFNMPM-_mNfpwNjcakjWT1gTnFgpggtiC=gDafDseFVcqfTuUg.mail.gmail.com> Content-Type: text/plain; charset="UTF-8" .Bill: Speed is not an issue in pytraj (users can use numpy or cython for C/Fortran speed). However, it will be hard for users to implement if they are not get used to do programming. :D Btw, we have Dan. And the enhancement in cpptraj automatically appear in pytraj. cheers Hai On Wed, Jul 12, 2017 at 6:07 PM, Bill Ross <ross.cgl.ucsf.edu> wrote: > Hi Guqin, > >> But I don't know for this method, how general it could be and >> how efficient it will be (considering the translation have to be done on >> all axes and iterations will be done on all mols/atoms...) I have no >> experience or idea. But I would love to follow up with updates if future >>cpptraj would have such changes. > > I don't know about python speed for such tasks. Likely optimizations are > possible. E.g. that inner 'if' I mentioned shouldn't be necessary, and > maybe something could be done with centroids of molecules. And one would > only calc inter-molecular distances, not the intra's since they would be > constant. > > It's just a suggestion on my part, since I'm not working in the field. > > Regards, > Bill > > On 7/12/17 2:54 PM, Guqin Shi wrote: >> Hi Bill, >> >> Thanks for your suggestion on this problem. Dan helped add a new option and >> seemingly solved the problem. (I am writing this email and saw your new >> reply just came in.) >> >> But I did go to check the "pytraj" and I am glad I did so. Previously I >> used cpptraj to get results and write separate python script to process or >> plot the data; but with pytraj it seems two steps could be merged into one. >> Although I didn't utilize pytraj to solve this problem but it's good to >> know it. >> >> As for your previous suggestion on image minimizer, I kinda get your idea. >> Because while Dan was developing the new option, I was using topotools in >> vmd to write protein coordinates from adjacent cells and picked out an >> intact hexamer manually. This is basically (from my understanding...) what >> you were mentioning: get translated images/coordinates and the molecules >> with the closest distance should theoretically be in the "correct" >> complex... But I don't know for this method, how general it could be and >> how efficient it will be (considering the translation have to be done on >> all axes and iterations will be done on all mols/atoms...) I have no >> experience or idea. But I would love to follow up with updates if future >> cpptraj would have such changes. >> >> Best, >> Guqin >> >> On Wed, Jul 12, 2017 at 5:37 PM, Bill Ross <ross.cgl.ucsf.edu> wrote: >> >>> I still wonder if my idea would be a more general solution, requiring no >>> thought on the user's part. >>> >>> Bill >>> >>> >>> On 7/12/17 2:34 PM, Guqin Shi wrote: >>>> Hi Dan, >>>> >>>> I want to let you know that I have tested the new option for my latest >>>> trajectories. It works very well so far. >>>> The default "autoimage" worked well until 86 ns that conventional way >>>> couldn't work anymore in my case. Then "autoimage" with "moveanchor" were >>>> performed on the following trajectories and so far so good. However, my >>>> simulation is still ongoing. So I will keep testing and report back until >>>> my simulation is done. >>>> >>>> As to the cpptraj tests, "make check" showed that all tests are passed. >>> So >>>> at least nothing I need to worry for now... >>>> >>>> >>>> Thanks a lot for your time and help! I am glad that my special system >>> help >>>> raise a new option... >>>> >>>> Best, >>>> Guqin >>>> >>>> On Wed, Jul 12, 2017 at 10:39 AM, Daniel Roe <daniel.r.roe.gmail.com> >>> wrote: >>>>> Hi, >>>>> >>>>> On Wed, Jul 12, 2017 at 10:32 AM, Guqin Shi <shi.293.osu.edu> wrote: >>>>>> I have multiple production run trajectories which have similar >>> problems. >>>>> I >>>>>> will test them one by one to see how things going. It might take a >>>>> while. I >>>>>> will report back hopefully by tomorrow. >>>>> Great - all feedback is appreciated! >>>>> >>>>>> When I installed cpptraj, there were some warnings. One of them is >>>>>> "Compilation with Sander API failed: (during ./configure). Others are >>>>> This is because your Amber installation is from Amber 14 and the >>>>> sander API has changed since then. Cpptraj's configure detects this >>>>> and disables the sander interface accordingly. >>>>> >>>>>> function warnings such as "unused variable" or "uninitialized" (during >>>>>> "make install"). I attached a file containing these warning messages. I >>>>> These warnings have to do with the 'readline' and 'xdr' libraries and >>>>> can be safely ignored. The real check is to 'make check' in >>>>> $CPPTRAJHOME or 'make test.all' in $CPPTRAJHOME/test. >>>>> >>>>> Hope this helps, >>>>> >>>>> -Dan >>>>> >>>>>> think the latter should be ok. As to the failure with sander API, is >>> this >>>>>> something I need to worry about considering future usage...? >>>>>> >>>>>> >>>>>> Thanks a lot for the help! Great start for today's work!! >>>>>> -Guqin >>>>>> >>>>>> On Wed, Jul 12, 2017 at 10:03 AM, Daniel Roe <daniel.r.roe.gmail.com> >>>>> wrote: >>>>>>> On Wed, Jul 12, 2017 at 9:55 AM, Guqin Shi <shi.293.osu.edu> wrote: >>>>>>>> Or maybe I can replace these two files under my current >>>>>>>> $AMBERHOME/AmberTools/src/cpptraj/src directory..? >>>>>>> This may not work. The GitHub version of cpptraj tends to diverge from >>>>>>> the AmberTools release pretty quickly. This can also mess up future >>>>>>> AmberTools updates. Just stick with the separate install for now. >>>>>>> >>>>>>> -Dan >>>>>>> >>>>>>>> Thanks, >>>>>>>> Guqin >>>>>>>> >>>>>>>> On Wed, Jul 12, 2017 at 8:07 AM, Daniel Roe <daniel.r.roe.gmail.com> >>>>>>> wrote: >>>>>>>>> Hi, >>>>>>>>> >>>>>>>>> The new option is live: https://github.com/Amber-MD/ >>> cpptraj/pull/515 >>>>>>>>> Just try adding the 'moveanchor' option to your 'autoimage' command. >>>>>>>>> It worked for the frames that you sent me. What it does is that when >>>>>>>>> imaging 'fixed' molecules it uses the previous molecule as the >>> anchor >>>>>>>>> point (the first fixed molecule uses the original anchor point). >>> This >>>>>>>>> probably will only work when molecules are both close in sequence >>> and >>>>>>>>> geometrically close. >>>>>>>>> >>>>>>>>> Try it and let me know if it works. >>>>>>>>> >>>>>>>>> -Dan >>>>>>>>> >>>>>>>>> On Tue, Jul 11, 2017 at 4:35 PM, Guqin Shi <shi.293.osu.edu> wrote: >>>>>>>>>> Oh my god...it just made my day... >>>>>>>>>> I've been desperately looking for solutions today... for example, >>>>> I am >>>>>>>>>> currently using the topotools plugged in VMD to write coordinates >>>>> of >>>>>>>>>> replicates from adjacent cells and trying to pick out the >>>>> coordinates >>>>>>> of >>>>>>>>> an >>>>>>>>>> intact complex...meantime I am worrying about the precision, the >>>>>>>>> potential >>>>>>>>>> artifacts, and speeds in processing massive of frames... >>>>>>>>>> >>>>>>>>>> -Guqin >>>>>>>>>> >>>>>>>>>> On Tue, Jul 11, 2017 at 3:52 PM, Daniel Roe < >>>>> daniel.r.roe.gmail.com> >>>>>>>>> wrote: >>>>>>>>>>> I think I have a fix (really a new autoimage option) that seems to >>>>>>>>>>> work. I'm testing now and will let you know when it's live. >>>>>>>>>>> >>>>>>>>>>> -Dan >>>>>>>>>>> >>>>>>>>>>> On Tue, Jul 11, 2017 at 11:46 AM, Guqin Shi <shi.293.osu.edu> >>>>> wrote: >>>>>>>>>>>> Hi Dan, >>>>>>>>>>>> >>>>>>>>>>>> this is really unfortunate but the unwrap doesn't work either... >>>>>>> The >>>>>>>>>>>> resulting coordinates are similar to autoimage/center-image that >>>>>>> one >>>>>>>>> of >>>>>>>>>>> the >>>>>>>>>>>> molecules is still left outside... >>>>>>>>>>>> In the Amber manual, there is a notation that "this command >>>>> fails >>>>>>> when >>>>>>>>>>> the >>>>>>>>>>>> masked molecules travel more than half of the box size within a >>>>>>> single >>>>>>>>>>>> frame." Is this the reason that unwrap couldn't work either...? >>>>>>>>>>>> >>>>>>>>>>>> I uploaded the raw coordinates of pr90 and the original input >>>>>>>>> coordinates >>>>>>>>>>>> pdb file into the folder. I also uploaded the an >>>>>>> test_unwrap_copy.in >>>>>>>>>>> file >>>>>>>>>>>> which contains the commands I used for reference-unwrap... I >>>>>>> comment >>>>>>>>> out >>>>>>>>>>>> center and image commands as since the unwrap failed, center and >>>>>>> image >>>>>>>>>>>> won't help much.. >>>>>>>>>>>> >>>>>>>>>>>> If you have time, would you mind having a look at >>>>> them...Thanks... >>>>>>>>>>>> Best, >>>>>>>>>>>> Guqin >>>>>>>>>>>> >>>>>>>>>>>> On Tue, Jul 11, 2017 at 9:00 AM, Daniel Roe < >>>>>>> daniel.r.roe.gmail.com> >>>>>>>>>>> wrote: >>>>>>>>>>>>> Wow - this is certainly a challenging system to image! No one >>>>>>>>> molecule >>>>>>>>>>>>> can be considered "center" - in fact, there isn't even a region >>>>>>> of a >>>>>>>>>>>>> molecule that can be considered to be the center since when the >>>>>>>>>>>>> hexamer is formed there is a large empty space in the center >>>>> (from >>>>>>>>>>>>> looking at the system this appears to be the way it should be >>>>>>>>>>>>> assembled). >>>>>>>>>>>>> >>>>>>>>>>>>> I'll have to think about the best way to address this. In the >>>>>>>>>>>>> meantime, here is a potential workaround. You could unwrap the >>>>>>> entire >>>>>>>>>>>>> trajectory using the original input coordinates as a reference >>>>>>>>>>>>> (assuming the hexamer is "properly" formed there). You would >>>>> have >>>>>>> to >>>>>>>>>>>>> make certain you unwrap the trajectory in the right order, >>>>> i.e. in >>>>>>>>> the >>>>>>>>>>>>> same order it was simulated. You can then center on the hexamer >>>>>>> but >>>>>>>>>>>>> *only* image the water (and ions). So e.g. >>>>>>>>>>>>> >>>>>>>>>>>>> parm 1P9M_Hexamer.prmtop >>>>>>>>>>>>> reference pr90.rst7 >>>>>>>>>>>>> trajin run0.nc >>>>>>>>>>>>> trajin run1.nc >>>>>>>>>>>>> ... >>>>>>>>>>>>> unwrap reference >>>>>>>>>>>>> center :1-1330 >>>>>>>>>>>>> image :WAT,Na+ >>>>>>>>>>>>> >>>>>>>>>>>>> The idea is to keep the hexamer together by effectively never >>>>>>> imaging >>>>>>>>>>>>> it, then reimaging all the mobile stuff so it looks nice. I >>>>> think >>>>>>>>>>>>> (hope) this will work. >>>>>>>>>>>>> >>>>>>>>>>>>> Thanks for the files! >>>>>>>>>>>>> >>>>>>>>>>>>> -Dan >>>>>>>>>>>>> >>>>>>>>>>>>> On Mon, Jul 10, 2017 at 1:05 PM, Guqin Shi <shi.293.osu.edu> >>>>>>> wrote: >>>>>>>>>>>>>> Hi Dan, >>>>>>>>>>>>>> >>>>>>>>>>>>>> In addition to visualize trajectories pleasantly...my main >>>>>>> purpose >>>>>>>>> is >>>>>>>>>>> to >>>>>>>>>>>>>> get correct coordinates so that the following MMPBSA >>>>> calculation >>>>>>>>>>> could be >>>>>>>>>>>>>> carried out... (or maybe MMPBSA doesn't care about that at >>>>>>>>> all...??? >>>>>>>>>>>>> then I >>>>>>>>>>>>>> was wasting lots of my time...) >>>>>>>>>>>>>> >>>>>>>>>>>>>> I attached a prmtop with solvents stripped and a 1 ns of >>>>>>>>>>>>> nowat_coordinates >>>>>>>>>>>>>> (for the sake of file size) which I keep having problem >>>>> imaging >>>>>>>>> it... >>>>>>>>>>> ( >>>>>>>>>>>>>> https://drive.google.com/open?id= >>>>> 0B7kncIsWo85uSWJmbFBtczNtdFE) >>>>>>>>> Please >>>>>>>>>>>>> let >>>>>>>>>>>>>> me know if you feel solvated coordinates are needed... >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> Thanks a lot!!! >>>>>>>>>>>>>> -Guqin >>>>>>>>>>>>>> >>>>>>>>>>>>>> On Mon, Jul 10, 2017 at 12:29 PM, Daniel Roe < >>>>>>>>> daniel.r.roe.gmail.com> >>>>>>>>>>>>> wrote: >>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> (Could you send me some coordinates to go along with that >>>>>>> topology >>>>>>>>>>>>> file?) >>>>>>>>>>>>>>> On Mon, Jul 10, 2017 at 12:15 PM, Guqin Shi < >>>>> shi.293.osu.edu> >>>>>>>>> wrote: >>>>>>>>>>>>>>>> at the bottom edge of box......According to the original >>>>>>> prmtop >>>>>>>>>>> files, >>>>>>>>>>>>>>> the >>>>>>>>>>>>>>>> complex sits at the center of water box, but also >>>>> meantime, >>>>>>> it >>>>>>>>> sits >>>>>>>>>>>>> along >>>>>>>>>>>>>>>> the diagonal line...It seems center-image puts molecule >>>>> along >>>>>>>>> any >>>>>>>>>>> of >>>>>>>>>>>>> the >>>>>>>>>>>>>>>> side line and that's why it just couldn't fit all back...? >>>>>>> But I >>>>>>>>>>> am so >>>>>>>>>>>>>>>> confused now as why early trajectories could be imaged >>>>>>> without >>>>>>>>> any >>>>>>>>>>>>>>>> problem... >>>>>>>>>>>>>>> Re-imaging is more of an art than a science, mostly because >>>>>>>>> imaging >>>>>>>>>>> is >>>>>>>>>>>>>>> something that we do to make things "look nice". The >>>>> molecules >>>>>>>>> being >>>>>>>>>>>>>>> simulated don't care where they are absolutely, they only >>>>> care >>>>>>>>> where >>>>>>>>>>>>>>> they are with respect to other molecules. When you center on >>>>>>> one >>>>>>>>>>>>>>> molecule, you shift the coordinates of the entire system, >>>>> some >>>>>>> of >>>>>>>>>>>>>>> which move past the boundaries of your unit cell. Those >>>>> atoms >>>>>>> are >>>>>>>>>>> then >>>>>>>>>>>>>>> "wrapped" or re-imaged back inside the unit cell, which is >>>>> what >>>>>>>>> can >>>>>>>>>>>>>>> result in molecules appearing "separated". The 'autoimage' >>>>>>> command >>>>>>>>>>>>>>> tries to image in a way that keeps these molecules together >>>>> by >>>>>>>>>>>>>>> defining an anchor molecule/region (which is at the center), >>>>>>> and >>>>>>>>>>>>>>> molecules that are "fixed" to that anchor - it then tries to >>>>>>>>> minimize >>>>>>>>>>>>>>> the distance between the anchor and fixed molecules. Where >>>>> this >>>>>>>>> fails >>>>>>>>>>>>>>> is when a "wrapped" version of the system has shorter >>>>> distances >>>>>>>>> than >>>>>>>>>>>>>>> the "unwrapped version", which is typically because the >>>>>>>>> definition of >>>>>>>>>>>>>>> the anchor (center) is off. This is why the definition of >>>>> the >>>>>>>>>>> "anchor" >>>>>>>>>>>>>>> region is so crucial. >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Send me those coordinates and I'll see what can be done. >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> -Dan >>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>>>> Guqin >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> On Mon, Jul 10, 2017 at 11:43 AM, Guqin Shi < >>>>>>> gshi.cop.ufl.edu> >>>>>>>>>>> wrote: >>>>>>>>>>>>>>>>> On Mon, Jul 10, 2017 at 8:32 AM, Daniel Roe < >>>>>>>>>>> daniel.r.roe.gmail.com> >>>>>>>>>>>>>>>>> wrote: >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> The key for 'autoimage' is that you need to specify a >>>>>>> region >>>>>>>>>>>>>>>>>> (molecule, residue, atom, etc) that visually you want to >>>>>>> be at >>>>>>>>>>> the >>>>>>>>>>>>>>>>>> center of your unit cell; in cpptraj this is called the >>>>>>>>>>> 'anchor'. By >>>>>>>>>>>>>>>>>> default 'autoimage' tries to use the first molecule to >>>>> do >>>>>>>>> this. >>>>>>>>>>>>>>>>>> However in certain systems another choice is better. For >>>>>>>>>>> example, if >>>>>>>>>>>>>>>>>> you have a dimer then you would want to choose 1 or more >>>>>>>>> residues >>>>>>>>>>>>> that >>>>>>>>>>>>>>>>>> are near the center of the interface between the two >>>>>>> monomers >>>>>>>>> as >>>>>>>>>>>>> your >>>>>>>>>>>>>>>>>> anchor. Without seeing your system I can't make specific >>>>>>>>>>>>>>>>>> recommendations, but you could try experimenting with >>>>>>>>> different >>>>>>>>>>>>> anchor >>>>>>>>>>>>>>>>>> points. If you'd like, send me a PDB file or >>>>>>> topology/restart >>>>>>>>>>> files >>>>>>>>>>>>> of >>>>>>>>>>>>>>>>>> your system off-list and I can try to recommend an >>>>> anchor. >>>>>>>>>>>>>>>>>> -Dan >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Hi Bill, >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Thanks for pointing out the key point of "autoimage". I >>>>>>> tried >>>>>>>>> to >>>>>>>>>>> play >>>>>>>>>>>>>>> with >>>>>>>>>>>>>>>>> autoimage-anchor a little bit by myself. I noticed that >>>>> the >>>>>>>>> mask >>>>>>>>>>> for >>>>>>>>>>>>>>>>> autoimage are molecule-wise, instead of residue-wise... >>>>>>>>> Therefore >>>>>>>>>>>>> when I >>>>>>>>>>>>>>>>> specify some center residues, cpptraj reports back with >>>>>>> error >>>>>>>>>>> (Error: >>>>>>>>>>>>>>>>> Anchor mask [:153-155] corresponds to 0 mols, should >>>>> only be >>>>>>>>> 1.) >>>>>>>>>>> and >>>>>>>>>>>>>>> then >>>>>>>>>>>>>>>>> it goes with default again... Maybe my syntax is somehow >>>>> not >>>>>>>>>>> correct? >>>>>>>>>>>>>>>>> Also, my system is a little bit special. It is a "dimer" >>>>> and >>>>>>>>> each >>>>>>>>>>>>>>> monomer >>>>>>>>>>>>>>>>> contains three molecules. There is a hollow in between >>>>> the >>>>>>> two >>>>>>>>>>>>> dimers... >>>>>>>>>>>>>>>>> Currently in my own practice, I picked three residues on >>>>>>> each >>>>>>>>> of >>>>>>>>>>> the >>>>>>>>>>>>>>> dimer >>>>>>>>>>>>>>>>> which I think, are the closest to the center of cell >>>>>>> (143-155 & >>>>>>>>>>>>>>> 818-820). >>>>>>>>>>>>>>>>> Also, since these residues are symmetric, I am not sure >>>>> how >>>>>>> the >>>>>>>>>>>>> program >>>>>>>>>>>>>>>>> would place them in terms of direction...or maybe in this >>>>>>> case, >>>>>>>>>>>>>>> asymmetric >>>>>>>>>>>>>>>>> residues might be better...? I attached the prmtop file >>>>>>> (with >>>>>>>>>>>>>>> solvens/ions) >>>>>>>>>>>>>>>>> here on my google drive: >>>>>>>>>>>>>>>>> https://drive.google.com/open?id= >>>>>>> 0B7kncIsWo85ud1BweGJfd1h1ZXM >>>>>>>>>>>>> (Since it >>>>>>>>>>>>>>>>> is quite big so I don't think mailing list server would >>>>>>> allow >>>>>>>>> that >>>>>>>>>>>>>>> size..) >>>>>>>>>>>>>>>>> Could you also check my system to see if my choice on >>>>>>> residues >>>>>>>>> are >>>>>>>>>>>>> good >>>>>>>>>>>>>>> or >>>>>>>>>>>>>>>>> maybe another set of residues are better..? >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Thanks a lot for your help! >>>>>>>>>>>>>>>>> -Guqin >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>> Guqin SHI >>>>>>>>>>>>>>>>> 1345 Center Drive >>>>>>>>>>>>>>>>> College of Pharmacy >>>>>>>>>>>>>>>>> PO Box 100485 >>>>>>>>>>>>>>>>> University of Florida >>>>>>>>>>>>>>>>> Gainesville, FL 32610 >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>> Guqin SHI >>>>>>>>>>>>>>>> PhD Candidate in Medicinal Chemistry and Pharmacognosy >>>>>>>>>>>>>>>> College of Pharmacy >>>>>>>>>>>>>>>> The Ohio State University >>>>>>>>>>>>>>>> Columbus, OH, 43210 >>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>> AMBER mailing list >>>>>>>>>>>>>>>> AMBER.ambermd.org >>>>>>>>>>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>> ------------------------- >>>>>>>>>>>>>>> Daniel R. Roe >>>>>>>>>>>>>>> Laboratory of Computational Biology >>>>>>>>>>>>>>> National Institutes of Health, NHLBI >>>>>>>>>>>>>>> 5635 Fishers Ln, Rm T900 >>>>>>>>>>>>>>> Rockville MD, 20852 >>>>>>>>>>>>>>> https://www.lobos.nih.gov/lcb >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>> AMBER mailing list >>>>>>>>>>>>>>> AMBER.ambermd.org >>>>>>>>>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber >>>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> -- >>>>>>>>>>>>>> Guqin SHI >>>>>>>>>>>>>> PhD Candidate in Medicinal Chemistry and Pharmacognosy >>>>>>>>>>>>>> College of Pharmacy >>>>>>>>>>>>>> The Ohio State University >>>>>>>>>>>>>> Columbus, OH, 43210 >>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>> AMBER mailing list >>>>>>>>>>>>>> AMBER.ambermd.org >>>>>>>>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber >>>>>>>>>>>>> >>>>>>>>>>>>> -- >>>>>>>>>>>>> ------------------------- >>>>>>>>>>>>> Daniel R. Roe >>>>>>>>>>>>> Laboratory of Computational Biology >>>>>>>>>>>>> National Institutes of Health, NHLBI >>>>>>>>>>>>> 5635 Fishers Ln, Rm T900 >>>>>>>>>>>>> Rockville MD, 20852 >>>>>>>>>>>>> https://www.lobos.nih.gov/lcb >>>>>>>>>>>>> >>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>> AMBER mailing list >>>>>>>>>>>>> AMBER.ambermd.org >>>>>>>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber >>>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> -- >>>>>>>>>>>> Guqin SHI >>>>>>>>>>>> PhD Candidate in Medicinal Chemistry and Pharmacognosy >>>>>>>>>>>> College of Pharmacy >>>>>>>>>>>> The Ohio State University >>>>>>>>>>>> Columbus, OH, 43210 >>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>> AMBER mailing list >>>>>>>>>>>> AMBER.ambermd.org >>>>>>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber >>>>>>>>>>> >>>>>>>>>>> -- >>>>>>>>>>> ------------------------- >>>>>>>>>>> Daniel R. Roe >>>>>>>>>>> Laboratory of Computational Biology >>>>>>>>>>> National Institutes of Health, NHLBI >>>>>>>>>>> 5635 Fishers Ln, Rm T900 >>>>>>>>>>> Rockville MD, 20852 >>>>>>>>>>> https://www.lobos.nih.gov/lcb >>>>>>>>>>> >>>>>>>>>>> _______________________________________________ >>>>>>>>>>> AMBER mailing list >>>>>>>>>>> AMBER.ambermd.org >>>>>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber >>>>>>>>>>> >>>>>>>>>> >>>>>>>>>> -- >>>>>>>>>> Guqin SHI >>>>>>>>>> PhD Candidate in Medicinal Chemistry and Pharmacognosy >>>>>>>>>> College of Pharmacy >>>>>>>>>> The Ohio State University >>>>>>>>>> Columbus, OH, 43210 >>>>>>>>>> _______________________________________________ >>>>>>>>>> AMBER mailing list >>>>>>>>>> AMBER.ambermd.org >>>>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber >>>>>>>>> >>>>>>>>> -- >>>>>>>>> ------------------------- >>>>>>>>> Daniel R. Roe >>>>>>>>> Laboratory of Computational Biology >>>>>>>>> National Institutes of Health, NHLBI >>>>>>>>> 5635 Fishers Ln, Rm T900 >>>>>>>>> Rockville MD, 20852 >>>>>>>>> https://www.lobos.nih.gov/lcb >>>>>>>>> >>>>>>>>> _______________________________________________ >>>>>>>>> AMBER mailing list >>>>>>>>> AMBER.ambermd.org >>>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber >>>>>>>>> >>>>>>>> >>>>>>>> -- >>>>>>>> Guqin SHI >>>>>>>> PhD Candidate in Medicinal Chemistry and Pharmacognosy >>>>>>>> College of Pharmacy >>>>>>>> The Ohio State University >>>>>>>> Columbus, OH, 43210 >>>>>>>> _______________________________________________ >>>>>>>> AMBER mailing list >>>>>>>> AMBER.ambermd.org >>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber >>>>>>> >>>>>>> -- >>>>>>> ------------------------- >>>>>>> Daniel R. Roe >>>>>>> Laboratory of Computational Biology >>>>>>> National Institutes of Health, NHLBI >>>>>>> 5635 Fishers Ln, Rm T900 >>>>>>> Rockville MD, 20852 >>>>>>> https://www.lobos.nih.gov/lcb >>>>>>> >>>>>>> _______________________________________________ >>>>>>> AMBER mailing list >>>>>>> AMBER.ambermd.org >>>>>>> http://lists.ambermd.org/mailman/listinfo/amber >>>>>>> >>>>>> >>>>>> -- >>>>>> Guqin SHI >>>>>> PhD Candidate in Medicinal Chemistry and Pharmacognosy >>>>>> College of Pharmacy >>>>>> The Ohio State University >>>>>> Columbus, OH, 43210 >>>>>> >>>>>> _______________________________________________ >>>>>> AMBER mailing list >>>>>> AMBER.ambermd.org >>>>>> http://lists.ambermd.org/mailman/listinfo/amber >>>>>> >>>>> >>>>> -- >>>>> ------------------------- >>>>> Daniel R. Roe >>>>> Laboratory of Computational Biology >>>>> National Institutes of Health, NHLBI >>>>> 5635 Fishers Ln, Rm T900 >>>>> Rockville MD, 20852 >>>>> https://www.lobos.nih.gov/lcb >>>>> >>>>> _______________________________________________ >>>>> AMBER mailing list >>>>> AMBER.ambermd.org >>>>> http://lists.ambermd.org/mailman/listinfo/amber >>>>> >>>> >>> >>> _______________________________________________ >>> AMBER mailing list >>> AMBER.ambermd.org >>> http://lists.ambermd.org/mailman/listinfo/amber >>> >> >> > > > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber ------------------------------ Message: 10 Date: Wed, 12 Jul 2017 18:20:12 -0400 From: Hai Nguyen <nhai.qn.gmail.com> Subject: Re: [AMBER] Suggestions about Center and Image for multiple-molecule complex To: AMBER Mailing List <amber.ambermd.org> Message-ID: <CAFNMPM-=8rB7K_tRAYYvOxw+ScSu5e_MmSpddmXEHQ_tsqbszw.mail.gmail.com> Content-Type: text/plain; charset="UTF-8" On Wed, Jul 12, 2017 at 5:54 PM, Guqin Shi <shi.293.osu.edu> wrote: > Hi Bill, > > Thanks for your suggestion on this problem. Dan helped add a new option and > seemingly solved the problem. (I am writing this email and saw your new > reply just came in.) > > But I did go to check the "pytraj" and I am glad I did so. Previously I > used cpptraj to get results and write separate python script to process or > plot the data; but with pytraj it seems two steps could be merged into one. > Although I didn't utilize pytraj to solve this problem but it's good to > know it. shameless ad: process, plot and visualization, https://github.com/arose/nglview/blob/master/README.md Hai > > As for your previous suggestion on image minimizer, I kinda get your idea. > Because while Dan was developing the new option, I was using topotools in > vmd to write protein coordinates from adjacent cells and picked out an > intact hexamer manually. This is basically (from my understanding...) what > you were mentioning: get translated images/coordinates and the molecules > with the closest distance should theoretically be in the "correct" > complex... But I don't know for this method, how general it could be and > how efficient it will be (considering the translation have to be done on > all axes and iterations will be done on all mols/atoms...) I have no > experience or idea. But I would love to follow up with updates if future > cpptraj would have such changes. > > Best, > Guqin > > On Wed, Jul 12, 2017 at 5:37 PM, Bill Ross <ross.cgl.ucsf.edu> wrote: > >> I still wonder if my idea would be a more general solution, requiring no >> thought on the user's part. >> >> Bill >> >> >> On 7/12/17 2:34 PM, Guqin Shi wrote: >> > Hi Dan, >> > >> > I want to let you know that I have tested the new option for my latest >> > trajectories. It works very well so far. >> > The default "autoimage" worked well until 86 ns that conventional way >> > couldn't work anymore in my case. Then "autoimage" with "moveanchor" were >> > performed on the following trajectories and so far so good. However, my >> > simulation is still ongoing. So I will keep testing and report back until >> > my simulation is done. >> > >> > As to the cpptraj tests, "make check" showed that all tests are passed. >> So >> > at least nothing I need to worry for now... >> > >> > >> > Thanks a lot for your time and help! I am glad that my special system >> help >> > raise a new option... >> > >> > Best, >> > Guqin >> > >> > On Wed, Jul 12, 2017 at 10:39 AM, Daniel Roe <daniel.r.roe.gmail.com> >> wrote: >> > >> >> Hi, >> >> >> >> On Wed, Jul 12, 2017 at 10:32 AM, Guqin Shi <shi.293.osu.edu> wrote: >> >>> I have multiple production run trajectories which have similar >> problems. >> >> I >> >>> will test them one by one to see how things going. It might take a >> >> while. I >> >>> will report back hopefully by tomorrow. >> >> Great - all feedback is appreciated! >> >> >> >>> When I installed cpptraj, there were some warnings. One of them is >> >>> "Compilation with Sander API failed: (during ./configure). Others are >> >> This is because your Amber installation is from Amber 14 and the >> >> sander API has changed since then. Cpptraj's configure detects this >> >> and disables the sander interface accordingly. >> >> >> >>> function warnings such as "unused variable" or "uninitialized" (during >> >>> "make install"). I attached a file containing these warning messages. I >> >> These warnings have to do with the 'readline' and 'xdr' libraries and >> >> can be safely ignored. The real check is to 'make check' in >> >> $CPPTRAJHOME or 'make test.all' in $CPPTRAJHOME/test. >> >> >> >> Hope this helps, >> >> >> >> -Dan >> >> >> >>> think the latter should be ok. As to the failure with sander API, is >> this >> >>> something I need to worry about considering future usage...? >> >>> >> >>> >> >>> Thanks a lot for the help! Great start for today's work!! >> >>> -Guqin >> >>> >> >>> On Wed, Jul 12, 2017 at 10:03 AM, Daniel Roe <daniel.r.roe.gmail.com> >> >> wrote: >> >>>> On Wed, Jul 12, 2017 at 9:55 AM, Guqin Shi <shi.293.osu.edu> wrote: >> >>>>> Or maybe I can replace these two files under my current >> >>>>> $AMBERHOME/AmberTools/src/cpptraj/src directory..? >> >>>> This may not work. The GitHub version of cpptraj tends to diverge from >> >>>> the AmberTools release pretty quickly. This can also mess up future >> >>>> AmberTools updates. Just stick with the separate install for now. >> >>>> >> >>>> -Dan >> >>>> >> >>>>> Thanks, >> >>>>> Guqin >> >>>>> >> >>>>> On Wed, Jul 12, 2017 at 8:07 AM, Daniel Roe <daniel.r.roe.gmail.com> >> >>>> wrote: >> >>>>>> Hi, >> >>>>>> >> >>>>>> The new option is live: https://github.com/Amber-MD/ >> cpptraj/pull/515 >> >>>>>> >> >>>>>> Just try adding the 'moveanchor' option to your 'autoimage' command. >> >>>>>> It worked for the frames that you sent me. What it does is that when >> >>>>>> imaging 'fixed' molecules it uses the previous molecule as the >> anchor >> >>>>>> point (the first fixed molecule uses the original anchor point). >> This >> >>>>>> probably will only work when molecules are both close in sequence >> and >> >>>>>> geometrically close. >> >>>>>> >> >>>>>> Try it and let me know if it works. >> >>>>>> >> >>>>>> -Dan >> >>>>>> >> >>>>>> On Tue, Jul 11, 2017 at 4:35 PM, Guqin Shi <shi.293.osu.edu> wrote: >> >>>>>>> Oh my god...it just made my day... >> >>>>>>> I've been desperately looking for solutions today... for example, >> >> I am >> >>>>>>> currently using the topotools plugged in VMD to write coordinates >> >> of >> >>>>>>> replicates from adjacent cells and trying to pick out the >> >> coordinates >> >>>> of >> >>>>>> an >> >>>>>>> intact complex...meantime I am worrying about the precision, the >> >>>>>> potential >> >>>>>>> artifacts, and speeds in processing massive of frames... >> >>>>>>> >> >>>>>>> -Guqin >> >>>>>>> >> >>>>>>> On Tue, Jul 11, 2017 at 3:52 PM, Daniel Roe < >> >> daniel.r.roe.gmail.com> >> >>>>>> wrote: >> >>>>>>>> I think I have a fix (really a new autoimage option) that seems to >> >>>>>>>> work. I'm testing now and will let you know when it's live. >> >>>>>>>> >> >>>>>>>> -Dan >> >>>>>>>> >> >>>>>>>> On Tue, Jul 11, 2017 at 11:46 AM, Guqin Shi <shi.293.osu.edu> >> >> wrote: >> >>>>>>>>> Hi Dan, >> >>>>>>>>> >> >>>>>>>>> this is really unfortunate but the unwrap doesn't work either... >> >>>> The >> >>>>>>>>> resulting coordinates are similar to autoimage/center-image that >> >>>> one >> >>>>>> of >> >>>>>>>> the >> >>>>>>>>> molecules is still left outside... >> >>>>>>>>> In the Amber manual, there is a notation that "this command >> >> fails >> >>>> when >> >>>>>>>> the >> >>>>>>>>> masked molecules travel more than half of the box size within a >> >>>> single >> >>>>>>>>> frame." Is this the reason that unwrap couldn't work either...? >> >>>>>>>>> >> >>>>>>>>> I uploaded the raw coordinates of pr90 and the original input >> >>>>>> coordinates >> >>>>>>>>> pdb file into the folder. I also uploaded the an >> >>>> test_unwrap_copy.in >> >>>>>>>> file >> >>>>>>>>> which contains the commands I used for reference-unwrap... I >> >>>> comment >> >>>>>> out >> >>>>>>>>> center and image commands as since the unwrap failed, center and >> >>>> image >> >>>>>>>>> won't help much.. >> >>>>>>>>> >> >>>>>>>>> If you have time, would you mind having a look at >> >> them...Thanks... >> >>>>>>>>> Best, >> >>>>>>>>> Guqin >> >>>>>>>>> >> >>>>>>>>> On Tue, Jul 11, 2017 at 9:00 AM, Daniel Roe < >> >>>> daniel.r.roe.gmail.com> >> >>>>>>>> wrote: >> >>>>>>>>>> Wow - this is certainly a challenging system to image! No one >> >>>>>> molecule >> >>>>>>>>>> can be considered "center" - in fact, there isn't even a region >> >>>> of a >> >>>>>>>>>> molecule that can be considered to be the center since when the >> >>>>>>>>>> hexamer is formed there is a large empty space in the center >> >> (from >> >>>>>>>>>> looking at the system this appears to be the way it should be >> >>>>>>>>>> assembled). >> >>>>>>>>>> >> >>>>>>>>>> I'll have to think about the best way to address this. In the >> >>>>>>>>>> meantime, here is a potential workaround. You could unwrap the >> >>>> entire >> >>>>>>>>>> trajectory using the original input coordinates as a reference >> >>>>>>>>>> (assuming the hexamer is "properly" formed there). You would >> >> have >> >>>> to >> >>>>>>>>>> make certain you unwrap the trajectory in the right order, >> >> i.e. in >> >>>>>> the >> >>>>>>>>>> same order it was simulated. You can then center on the hexamer >> >>>> but >> >>>>>>>>>> *only* image the water (and ions). So e.g. >> >>>>>>>>>> >> >>>>>>>>>> parm 1P9M_Hexamer.prmtop >> >>>>>>>>>> reference pr90.rst7 >> >>>>>>>>>> trajin run0.nc >> >>>>>>>>>> trajin run1.nc >> >>>>>>>>>> ... >> >>>>>>>>>> unwrap reference >> >>>>>>>>>> center :1-1330 >> >>>>>>>>>> image :WAT,Na+ >> >>>>>>>>>> >> >>>>>>>>>> The idea is to keep the hexamer together by effectively never >> >>>> imaging >> >>>>>>>>>> it, then reimaging all the mobile stuff so it looks nice. I >> >> think >> >>>>>>>>>> (hope) this will work. >> >>>>>>>>>> >> >>>>>>>>>> Thanks for the files! >> >>>>>>>>>> >> >>>>>>>>>> -Dan >> >>>>>>>>>> >> >>>>>>>>>> On Mon, Jul 10, 2017 at 1:05 PM, Guqin Shi <shi.293.osu.edu> >> >>>> wrote: >> >>>>>>>>>>> Hi Dan, >> >>>>>>>>>>> >> >>>>>>>>>>> In addition to visualize trajectories pleasantly...my main >> >>>> purpose >> >>>>>> is >> >>>>>>>> to >> >>>>>>>>>>> get correct coordinates so that the following MMPBSA >> >> calculation >> >>>>>>>> could be >> >>>>>>>>>>> carried out... (or maybe MMPBSA doesn't care about that at >> >>>>>> all...??? >> >>>>>>>>>> then I >> >>>>>>>>>>> was wasting lots of my time...) >> >>>>>>>>>>> >> >>>>>>>>>>> I attached a prmtop with solvents stripped and a 1 ns of >> >>>>>>>>>> nowat_coordinates >> >>>>>>>>>>> (for the sake of file size) which I keep having problem >> >> imaging >> >>>>>> it... >> >>>>>>>> ( >> >>>>>>>>>>> https://drive.google.com/open?id= >> >> 0B7kncIsWo85uSWJmbFBtczNtdFE) >> >>>>>> Please >> >>>>>>>>>> let >> >>>>>>>>>>> me know if you feel solvated coordinates are needed... >> >>>>>>>>>>> >> >>>>>>>>>>> >> >>>>>>>>>>> Thanks a lot!!! >> >>>>>>>>>>> -Guqin >> >>>>>>>>>>> >> >>>>>>>>>>> On Mon, Jul 10, 2017 at 12:29 PM, Daniel Roe < >> >>>>>> daniel.r.roe.gmail.com> >> >>>>>>>>>> wrote: >> >>>>>>>>>>>> Hi, >> >>>>>>>>>>>> >> >>>>>>>>>>>> (Could you send me some coordinates to go along with that >> >>>> topology >> >>>>>>>>>> file?) >> >>>>>>>>>>>> On Mon, Jul 10, 2017 at 12:15 PM, Guqin Shi < >> >> shi.293.osu.edu> >> >>>>>> wrote: >> >>>>>>>>>>>>> at the bottom edge of box......According to the original >> >>>> prmtop >> >>>>>>>> files, >> >>>>>>>>>>>> the >> >>>>>>>>>>>>> complex sits at the center of water box, but also >> >> meantime, >> >>>> it >> >>>>>> sits >> >>>>>>>>>> along >> >>>>>>>>>>>>> the diagonal line...It seems center-image puts molecule >> >> along >> >>>>>> any >> >>>>>>>> of >> >>>>>>>>>> the >> >>>>>>>>>>>>> side line and that's why it just couldn't fit all back...? >> >>>> But I >> >>>>>>>> am so >> >>>>>>>>>>>>> confused now as why early trajectories could be imaged >> >>>> without >> >>>>>> any >> >>>>>>>>>>>>> problem... >> >>>>>>>>>>>> Re-imaging is more of an art than a science, mostly because >> >>>>>> imaging >> >>>>>>>> is >> >>>>>>>>>>>> something that we do to make things "look nice". The >> >> molecules >> >>>>>> being >> >>>>>>>>>>>> simulated don't care where they are absolutely, they only >> >> care >> >>>>>> where >> >>>>>>>>>>>> they are with respect to other molecules. When you center on >> >>>> one >> >>>>>>>>>>>> molecule, you shift the coordinates of the entire system, >> >> some >> >>>> of >> >>>>>>>>>>>> which move past the boundaries of your unit cell. Those >> >> atoms >> >>>> are >> >>>>>>>> then >> >>>>>>>>>>>> "wrapped" or re-imaged back inside the unit cell, which is >> >> what >> >>>>>> can >> >>>>>>>>>>>> result in molecules appearing "separated". The 'autoimage' >> >>>> command >> >>>>>>>>>>>> tries to image in a way that keeps these molecules together >> >> by >> >>>>>>>>>>>> defining an anchor molecule/region (which is at the center), >> >>>> and >> >>>>>>>>>>>> molecules that are "fixed" to that anchor - it then tries to >> >>>>>> minimize >> >>>>>>>>>>>> the distance between the anchor and fixed molecules. Where >> >> this >> >>>>>> fails >> >>>>>>>>>>>> is when a "wrapped" version of the system has shorter >> >> distances >> >>>>>> than >> >>>>>>>>>>>> the "unwrapped version", which is typically because the >> >>>>>> definition of >> >>>>>>>>>>>> the anchor (center) is off. This is why the definition of >> >> the >> >>>>>>>> "anchor" >> >>>>>>>>>>>> region is so crucial. >> >>>>>>>>>>>> >> >>>>>>>>>>>> Send me those coordinates and I'll see what can be done. >> >>>>>>>>>>>> >> >>>>>>>>>>>> -Dan >> >>>>>>>>>>>> >> >>>>>>>>>>>>> >> >>>>>>>>>>>>> Thanks, >> >>>>>>>>>>>>> Guqin >> >>>>>>>>>>>>> >> >>>>>>>>>>>>> On Mon, Jul 10, 2017 at 11:43 AM, Guqin Shi < >> >>>> gshi.cop.ufl.edu> >> >>>>>>>> wrote: >> >>>>>>>>>>>>>> On Mon, Jul 10, 2017 at 8:32 AM, Daniel Roe < >> >>>>>>>> daniel.r.roe.gmail.com> >> >>>>>>>>>>>>>> wrote: >> >>>>>>>>>>>>>> >> >>>>>>>>>>>>>>> Hi, >> >>>>>>>>>>>>>>> >> >>>>>>>>>>>>>>> The key for 'autoimage' is that you need to specify a >> >>>> region >> >>>>>>>>>>>>>>> (molecule, residue, atom, etc) that visually you want to >> >>>> be at >> >>>>>>>> the >> >>>>>>>>>>>>>>> center of your unit cell; in cpptraj this is called the >> >>>>>>>> 'anchor'. By >> >>>>>>>>>>>>>>> default 'autoimage' tries to use the first molecule to >> >> do >> >>>>>> this. >> >>>>>>>>>>>>>>> However in certain systems another choice is better. For >> >>>>>>>> example, if >> >>>>>>>>>>>>>>> you have a dimer then you would want to choose 1 or more >> >>>>>> residues >> >>>>>>>>>> that >> >>>>>>>>>>>>>>> are near the center of the interface between the two >> >>>> monomers >> >>>>>> as >> >>>>>>>>>> your >> >>>>>>>>>>>>>>> anchor. Without seeing your system I can't make specific >> >>>>>>>>>>>>>>> recommendations, but you could try experimenting with >> >>>>>> different >> >>>>>>>>>> anchor >> >>>>>>>>>>>>>>> points. If you'd like, send me a PDB file or >> >>>> topology/restart >> >>>>>>>> files >> >>>>>>>>>> of >> >>>>>>>>>>>>>>> your system off-list and I can try to recommend an >> >> anchor. >> >>>>>>>>>>>>>>> -Dan >> >>>>>>>>>>>>>>> >> >>>>>>>>>>>>>>> >> >>>>>>>>>>>>>> Hi Bill, >> >>>>>>>>>>>>>> >> >>>>>>>>>>>>>> Thanks for pointing out the key point of "autoimage". I >> >>>> tried >> >>>>>> to >> >>>>>>>> play >> >>>>>>>>>>>> with >> >>>>>>>>>>>>>> autoimage-anchor a little bit by myself. I noticed that >> >> the >> >>>>>> mask >> >>>>>>>> for >> >>>>>>>>>>>>>> autoimage are molecule-wise, instead of residue-wise... >> >>>>>> Therefore >> >>>>>>>>>> when I >> >>>>>>>>>>>>>> specify some center residues, cpptraj reports back with >> >>>> error >> >>>>>>>> (Error: >> >>>>>>>>>>>>>> Anchor mask [:153-155] corresponds to 0 mols, should >> >> only be >> >>>>>> 1.) >> >>>>>>>> and >> >>>>>>>>>>>> then >> >>>>>>>>>>>>>> it goes with default again... Maybe my syntax is somehow >> >> not >> >>>>>>>> correct? >> >>>>>>>>>>>>>> Also, my system is a little bit special. It is a "dimer" >> >> and >> >>>>>> each >> >>>>>>>>>>>> monomer >> >>>>>>>>>>>>>> contains three molecules. There is a hollow in between >> >> the >> >>>> two >> >>>>>>>>>> dimers... >> >>>>>>>>>>>>>> Currently in my own practice, I picked three residues on >> >>>> each >> >>>>>> of >> >>>>>>>> the >> >>>>>>>>>>>> dimer >> >>>>>>>>>>>>>> which I think, are the closest to the center of cell >> >>>> (143-155 & >> >>>>>>>>>>>> 818-820). >> >>>>>>>>>>>>>> Also, since these residues are symmetric, I am not sure >> >> how >> >>>> the >> >>>>>>>>>> program >> >>>>>>>>>>>>>> would place them in terms of direction...or maybe in this >> >>>> case, >> >>>>>>>>>>>> asymmetric >> >>>>>>>>>>>>>> residues might be better...? I attached the prmtop file >> >>>> (with >> >>>>>>>>>>>> solvens/ions) >> >>>>>>>>>>>>>> here on my google drive: >> >>>>>>>>>>>>>> https://drive.google.com/open?id= >> >>>> 0B7kncIsWo85ud1BweGJfd1h1ZXM >> >>>>>>>>>> (Since it >> >>>>>>>>>>>>>> is quite big so I don't think mailing list server would >> >>>> allow >> >>>>>> that >> >>>>>>>>>>>> size..) >> >>>>>>>>>>>>>> Could you also check my system to see if my choice on >> >>>> residues >> >>>>>> are >> >>>>>>>>>> good >> >>>>>>>>>>>> or >> >>>>>>>>>>>>>> maybe another set of residues are better..? >> >>>>>>>>>>>>>> >> >>>>>>>>>>>>>> >> >>>>>>>>>>>>>> Thanks a lot for your help! >> >>>>>>>>>>>>>> -Guqin >> >>>>>>>>>>>>>> >> >>>>>>>>>>>>>> -- >> >>>>>>>>>>>>>> Guqin SHI >> >>>>>>>>>>>>>> 1345 Center Drive >> >>>>>>>>>>>>>> College of Pharmacy >> >>>>>>>>>>>>>> PO Box 100485 >> >>>>>>>>>>>>>> University of Florida >> >>>>>>>>>>>>>> Gainesville, FL 32610 >> >>>>>>>>>>>>>> >> >>>>>>>>>>>>> >> >>>>>>>>>>>>> >> >>>>>>>>>>>>> -- >> >>>>>>>>>>>>> Guqin SHI >> >>>>>>>>>>>>> PhD Candidate in Medicinal Chemistry and Pharmacognosy >> >>>>>>>>>>>>> College of Pharmacy >> >>>>>>>>>>>>> The Ohio State University >> >>>>>>>>>>>>> Columbus, OH, 43210 >> >>>>>>>>>>>>> _______________________________________________ >> >>>>>>>>>>>>> AMBER mailing list >> >>>>>>>>>>>>> AMBER.ambermd.org >> >>>>>>>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber >> >>>>>>>>>>>> >> >>>>>>>>>>>> >> >>>>>>>>>>>> -- >> >>>>>>>>>>>> ------------------------- >> >>>>>>>>>>>> Daniel R. Roe >> >>>>>>>>>>>> Laboratory of Computational Biology >> >>>>>>>>>>>> National Institutes of Health, NHLBI >> >>>>>>>>>>>> 5635 Fishers Ln, Rm T900 >> >>>>>>>>>>>> Rockville MD, 20852 >> >>>>>>>>>>>> https://www.lobos.nih.gov/lcb >> >>>>>>>>>>>> >> >>>>>>>>>>>> _______________________________________________ >> >>>>>>>>>>>> AMBER mailing list >> >>>>>>>>>>>> AMBER.ambermd.org >> >>>>>>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber >> >>>>>>>>>>>> >> >>>>>>>>>>> >> >>>>>>>>>>> >> >>>>>>>>>>> -- >> >>>>>>>>>>> Guqin SHI >> >>>>>>>>>>> PhD Candidate in Medicinal Chemistry and Pharmacognosy >> >>>>>>>>>>> College of Pharmacy >> >>>>>>>>>>> The Ohio State University >> >>>>>>>>>>> Columbus, OH, 43210 >> >>>>>>>>>>> _______________________________________________ >> >>>>>>>>>>> AMBER mailing list >> >>>>>>>>>>> AMBER.ambermd.org >> >>>>>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber >> >>>>>>>>>> >> >>>>>>>>>> >> >>>>>>>>>> -- >> >>>>>>>>>> ------------------------- >> >>>>>>>>>> Daniel R. Roe >> >>>>>>>>>> Laboratory of Computational Biology >> >>>>>>>>>> National Institutes of Health, NHLBI >> >>>>>>>>>> 5635 Fishers Ln, Rm T900 >> >>>>>>>>>> Rockville MD, 20852 >> >>>>>>>>>> https://www.lobos.nih.gov/lcb >> >>>>>>>>>> >> >>>>>>>>>> _______________________________________________ >> >>>>>>>>>> AMBER mailing list >> >>>>>>>>>> AMBER.ambermd.org >> >>>>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber >> >>>>>>>>>> >> >>>>>>>>> >> >>>>>>>>> >> >>>>>>>>> -- >> >>>>>>>>> Guqin SHI >> >>>>>>>>> PhD Candidate in Medicinal Chemistry and Pharmacognosy >> >>>>>>>>> College of Pharmacy >> >>>>>>>>> The Ohio State University >> >>>>>>>>> Columbus, OH, 43210 >> >>>>>>>>> _______________________________________________ >> >>>>>>>>> AMBER mailing list >> >>>>>>>>> AMBER.ambermd.org >> >>>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber >> >>>>>>>> >> >>>>>>>> >> >>>>>>>> -- >> >>>>>>>> ------------------------- >> >>>>>>>> Daniel R. Roe >> >>>>>>>> Laboratory of Computational Biology >> >>>>>>>> National Institutes of Health, NHLBI >> >>>>>>>> 5635 Fishers Ln, Rm T900 >> >>>>>>>> Rockville MD, 20852 >> >>>>>>>> https://www.lobos.nih.gov/lcb >> >>>>>>>> >> >>>>>>>> _______________________________________________ >> >>>>>>>> AMBER mailing list >> >>>>>>>> AMBER.ambermd.org >> >>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber >> >>>>>>>> >> >>>>>>> >> >>>>>>> >> >>>>>>> -- >> >>>>>>> Guqin SHI >> >>>>>>> PhD Candidate in Medicinal Chemistry and Pharmacognosy >> >>>>>>> College of Pharmacy >> >>>>>>> The Ohio State University >> >>>>>>> Columbus, OH, 43210 >> >>>>>>> _______________________________________________ >> >>>>>>> AMBER mailing list >> >>>>>>> AMBER.ambermd.org >> >>>>>>> http://lists.ambermd.org/mailman/listinfo/amber >> >>>>>> >> >>>>>> >> >>>>>> -- >> >>>>>> ------------------------- >> >>>>>> Daniel R. Roe >> >>>>>> Laboratory of Computational Biology >> >>>>>> National Institutes of Health, NHLBI >> >>>>>> 5635 Fishers Ln, Rm T900 >> >>>>>> Rockville MD, 20852 >> >>>>>> https://www.lobos.nih.gov/lcb >> >>>>>> >> >>>>>> _______________________________________________ >> >>>>>> AMBER mailing list >> >>>>>> AMBER.ambermd.org >> >>>>>> http://lists.ambermd.org/mailman/listinfo/amber >> >>>>>> >> >>>>> >> >>>>> >> >>>>> -- >> >>>>> Guqin SHI >> >>>>> PhD Candidate in Medicinal Chemistry and Pharmacognosy >> >>>>> College of Pharmacy >> >>>>> The Ohio State University >> >>>>> Columbus, OH, 43210 >> >>>>> _______________________________________________ >> >>>>> AMBER mailing list >> >>>>> AMBER.ambermd.org >> >>>>> http://lists.ambermd.org/mailman/listinfo/amber >> >>>> >> >>>> >> >>>> -- >> >>>> ------------------------- >> >>>> Daniel R. Roe >> >>>> Laboratory of Computational Biology >> >>>> National Institutes of Health, NHLBI >> >>>> 5635 Fishers Ln, Rm T900 >> >>>> Rockville MD, 20852 >> >>>> https://www.lobos.nih.gov/lcb >> >>>> >> >>>> _______________________________________________ >> >>>> AMBER mailing list >> >>>> AMBER.ambermd.org >> >>>> http://lists.ambermd.org/mailman/listinfo/amber >> >>>> >> >>> >> >>> >> >>> -- >> >>> Guqin SHI >> >>> PhD Candidate in Medicinal Chemistry and Pharmacognosy >> >>> College of Pharmacy >> >>> The Ohio State University >> >>> Columbus, OH, 43210 >> >>> >> >>> _______________________________________________ >> >>> AMBER mailing list >> >>> AMBER.ambermd.org >> >>> http://lists.ambermd.org/mailman/listinfo/amber >> >>> >> >> >> >> >> >> -- >> >> ------------------------- >> >> Daniel R. Roe >> >> Laboratory of Computational Biology >> >> National Institutes of Health, NHLBI >> >> 5635 Fishers Ln, Rm T900 >> >> Rockville MD, 20852 >> >> https://www.lobos.nih.gov/lcb >> >> >> >> _______________________________________________ >> >> AMBER mailing list >> >> AMBER.ambermd.org >> >> http://lists.ambermd.org/mailman/listinfo/amber >> >> >> > >> > >> >> >> _______________________________________________ >> AMBER mailing list >> AMBER.ambermd.org >> http://lists.ambermd.org/mailman/listinfo/amber >> > > > > -- > Guqin SHI > PhD Candidate in Medicinal Chemistry and Pharmacognosy > College of Pharmacy > The Ohio State University > Columbus, OH, 43210 > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber ------------------------------ Message: 11 Date: Wed, 12 Jul 2017 15:36:52 -0700 From: Bill Ross <ross.cgl.ucsf.edu> Subject: Re: [AMBER] Suggestions about Center and Image for multiple-molecule complex To: amber.ambermd.org Message-ID: <59949ef1-244c-f4a1-1fbf-40073ed374bf.cgl.ucsf.edu> Content-Type: text/plain; charset=utf-8; format=flowed Very cool package, as you can see in my live MD demo: http://phobrain.com/pr/home/mol.html Bill On 7/12/17 3:20 PM, Hai Nguyen wrote: > shameless ad: process, plot and visualization, > https://github.com/arose/nglview/blob/master/README.md ------------------------------ Message: 12 Date: Wed, 12 Jul 2017 22:40:42 +0000 From: "Krantzman, Kristin D" <KrantzmanK.cofc.edu> Subject: [AMBER] Problem with running mdout_analyzer.py To: AMBER Mailing List <amber.ambermd.org> Message-ID: <CY1PR0401MB1066985D2BEE0628425C8E4FB8AF0.CY1PR0401MB1066.namprd04.prod.outlook.com> Content-Type: text/plain; charset="us-ascii" Greetings AMBER users, I am trying to run mdout_analyzer.py and get the following error: Traceback (most recent call last): File "./mdout_analyzer.py", line 48, in <module> root = Tk() File "/usr/local/amber16/miniconda/lib/python2.7/lib-tk/Tkinter.py", line 1820, in __init__ self.tk = _tkinter.create(screenName, baseName, className, interactive, wantobjects, useTk, sync, use) _tkinter.TclError: Can't find a usable init.tcl in the following directories: /opt/anaconda1anaconda2anaconda3/lib/tcl8.5 /usr/local/amber16/lib/tcl8.5 /usr/local/lib/tcl8.5 /usr/local/amber16/library /usr/local/library /usr/local/tcl8.5.18/library /usr/tcl8.5.18/library I reinstalled tcl, I still get this error. Could you help with this? Best, Kristin This probably means that Tcl wasn't installed properly. Kristin D. Krantzman Professor, Department of Chemistry and Biochemistry College of Charleston Charleston, SC 29424 (843) 953-3378 ------------------------------ Message: 13 Date: Wed, 12 Jul 2017 15:43:02 -0700 From: Bill Ross <ross.cgl.ucsf.edu> Subject: Re: [AMBER] Problem with running mdout_analyzer.py To: amber.ambermd.org Message-ID: <25290a26-e804-7a73-2a76-d25c8051aac4.cgl.ucsf.edu> Content-Type: text/plain; charset=utf-8; format=flowed > /opt/anaconda1anaconda2anaconda3/lib/tcl8.5 That path sure looks like a broken install, but I don't know anything about anaconda. Bill On 7/12/17 3:40 PM, Krantzman, Kristin D wrote: > Greetings AMBER users, > I am trying to run mdout_analyzer.py and get the following error: > Traceback (most recent call last): > File "./mdout_analyzer.py", line 48, in <module> > root = Tk() > File "/usr/local/amber16/miniconda/lib/python2.7/lib-tk/Tkinter.py", line 1820, in __init__ > self.tk = _tkinter.create(screenName, baseName, className, interactive, wantobjects, useTk, sync, use) > _tkinter.TclError: Can't find a usable init.tcl in the following directories: > /opt/anaconda1anaconda2anaconda3/lib/tcl8.5 /usr/local/amber16/lib/tcl8.5 /usr/local/lib/tcl8.5 /usr/local/amber16/library /usr/local/library /usr/local/tcl8.5.18/library /usr/tcl8.5.18/library > I reinstalled tcl, I still get this error. Could you help with this? > Best, Kristin > > > This probably means that Tcl wasn't installed properly. > Kristin D. Krantzman > Professor, Department of Chemistry and Biochemistry > College of Charleston > Charleston, SC 29424 > (843) 953-3378 > > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber ------------------------------ Message: 14 Date: Wed, 12 Jul 2017 15:44:56 -0700 From: Bill Ross <ross.cgl.ucsf.edu> Subject: Re: [AMBER] Problem with running mdout_analyzer.py To: amber.ambermd.org Message-ID: <2e0a4da1-8428-fa14-6a5a-a8fd6344d901.cgl.ucsf.edu> Content-Type: text/plain; charset=utf-8; format=flowed Correction - not a broken install, but a broken config that is concatenating names instead of choosing one. Bill On 7/12/17 3:43 PM, Bill Ross wrote: > > /opt/anaconda1anaconda2anaconda3/lib/tcl8.5 > > That path sure looks like a broken install, but I don't know anything > about anaconda. > > Bill > > On 7/12/17 3:40 PM, Krantzman, Kristin D wrote: >> Greetings AMBER users, >> I am trying to run mdout_analyzer.py and get the following error: >> Traceback (most recent call last): >> File "./mdout_analyzer.py", line 48, in <module> >> root = Tk() >> File "/usr/local/amber16/miniconda/lib/python2.7/lib-tk/Tkinter.py", line 1820, in __init__ >> self.tk = _tkinter.create(screenName, baseName, className, interactive, wantobjects, useTk, sync, use) >> _tkinter.TclError: Can't find a usable init.tcl in the following directories: >> /opt/anaconda1anaconda2anaconda3/lib/tcl8.5 /usr/local/amber16/lib/tcl8.5 /usr/local/lib/tcl8.5 /usr/local/amber16/library /usr/local/library /usr/local/tcl8.5.18/library /usr/tcl8.5.18/library >> I reinstalled tcl, I still get this error. Could you help with this? >> Best, Kristin >> >> >> This probably means that Tcl wasn't installed properly. >> Kristin D. Krantzman >> Professor, Department of Chemistry and Biochemistry >> College of Charleston >> Charleston, SC 29424 >> (843) 953-3378 >> >> _______________________________________________ >> AMBER mailing list >> AMBER.ambermd.org >> http://lists.ambermd.org/mailman/listinfo/amber > > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber ------------------------------ Message: 15 Date: Wed, 12 Jul 2017 22:55:41 +0000 From: "Krantzman, Kristin D" <KrantzmanK.cofc.edu> Subject: Re: [AMBER] Problem with running mdout_analyzer.py To: AMBER Mailing List <amber.ambermd.org> Message-ID: <CY1PR0401MB10667A30E5262A9E6A663EDBB8AF0.CY1PR0401MB1066.namprd04.prod.outlook.com> Content-Type: text/plain; charset="us-ascii" Hi Bill, Python is automatically installed when I type "make install" with AmberTools16. I do not know how to find the configuration file that has the error. Kristin -----Original Message----- From: Bill Ross [mailto:ross.cgl.ucsf.edu] Sent: Wednesday, July 12, 2017 6:45 PM To: amber.ambermd.org Subject: Re: [AMBER] Problem with running mdout_analyzer.py Correction - not a broken install, but a broken config that is concatenating names instead of choosing one. Bill On 7/12/17 3:43 PM, Bill Ross wrote: > > /opt/anaconda1anaconda2anaconda3/lib/tcl8.5 > > That path sure looks like a broken install, but I don't know anything > about anaconda. > > Bill > > On 7/12/17 3:40 PM, Krantzman, Kristin D wrote: >> Greetings AMBER users, >> I am trying to run mdout_analyzer.py and get the following error: >> Traceback (most recent call last): >> File "./mdout_analyzer.py", line 48, in <module> >> root = Tk() >> File "/usr/local/amber16/miniconda/lib/python2.7/lib-tk/Tkinter.py", line 1820, in __init__ >> self.tk = _tkinter.create(screenName, baseName, className, >> interactive, wantobjects, useTk, sync, use) >> _tkinter.TclError: Can't find a usable init.tcl in the following directories: >> /opt/anaconda1anaconda2anaconda3/lib/tcl8.5 >> /usr/local/amber16/lib/tcl8.5 /usr/local/lib/tcl8.5 /usr/local/amber16/library /usr/local/library /usr/local/tcl8.5.18/library /usr/tcl8.5.18/library I reinstalled tcl, I still get this error. Could you help with this? >> Best, Kristin >> >> >> This probably means that Tcl wasn't installed properly. >> Kristin D. Krantzman >> Professor, Department of Chemistry and Biochemistry College of >> Charleston Charleston, SC 29424 >> (843) 953-3378 >> >> _______________________________________________ >> AMBER mailing list >> AMBER.ambermd.org >> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org >> _mailman_listinfo_amber&d=DwICAg&c=7MSSWy9Bs2yocjNQzurxOQ&r=rDr-VDoXC >> Kpr5ouXXYSZkHF6q5gU19w8m7W8WZccZ7U&m=05GA69kYpADyAfYrZgotQ_jPUCJfvrw7 >> ZdtuDC7nbNI&s=v8nAsRTANLujksAhkfYwDGyLppXkweYL1R6TmLUC-7w&e= > > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org_ > mailman_listinfo_amber&d=DwICAg&c=7MSSWy9Bs2yocjNQzurxOQ&r=rDr-VDoXCKp > r5ouXXYSZkHF6q5gU19w8m7W8WZccZ7U&m=05GA69kYpADyAfYrZgotQ_jPUCJfvrw7Zdt > uDC7nbNI&s=v8nAsRTANLujksAhkfYwDGyLppXkweYL1R6TmLUC-7w&e= _______________________________________________ AMBER mailing list AMBER.ambermd.org https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org_mailman_listinfo_amber&d=DwICAg&c=7MSSWy9Bs2yocjNQzurxOQ&r=rDr-VDoXCKpr5ouXXYSZkHF6q5gU19w8m7W8WZccZ7U&m=05GA69kYpADyAfYrZgotQ_jPUCJfvrw7ZdtuDC7nbNI&s=v8nAsRTANLujksAhkfYwDGyLppXkweYL1R6TmLUC-7w&e= ------------------------------ Message: 16 Date: Wed, 12 Jul 2017 18:57:26 -0400 From: Guqin Shi <shi.293.osu.edu> Subject: Re: [AMBER] Suggestions about Center and Image for multiple-molecule complex To: AMBER Mailing List <amber.ambermd.org> Message-ID: <CACUf8HdRkvrvE57vhp+c_f-Ruqaz9=2fQNPQ73mO_sKipNq_ZQ.mail.gmail.com> Content-Type: text/plain; charset="UTF-8" Bill and Hai, Thanks for those ads, LOL. On Wed, Jul 12, 2017 at 6:36 PM, Bill Ross <ross.cgl.ucsf.edu> wrote: > Very cool package, as you can see in my live MD demo: > > http://phobrain.com/pr/home/mol.html > > Bill > > On 7/12/17 3:20 PM, Hai Nguyen wrote: > > shameless ad: process, plot and visualization, > > https://github.com/arose/nglview/blob/master/README.md > > > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber > -- Guqin SHI PhD Candidate in Medicinal Chemistry and Pharmacognosy College of Pharmacy The Ohio State University Columbus, OH, 43210 ------------------------------ Message: 17 Date: Wed, 12 Jul 2017 16:02:02 -0700 From: Bill Ross <ross.cgl.ucsf.edu> Subject: Re: [AMBER] Problem with running mdout_analyzer.py To: amber.ambermd.org Message-ID: <a581150a-fc0d-3d7e-d0af-752f64ea2655.cgl.ucsf.edu> Content-Type: text/plain; charset=utf-8; format=flowed Hi Kristin, Try $ env and see if there are any clues. Probably a variable with a name including LIB points there, and from that we may reason backwards from general principles, absent expert help. Bill On 7/12/17 3:55 PM, Krantzman, Kristin D wrote: > Hi Bill, > Python is automatically installed when I type "make install" with AmberTools16. I do not know how to find the configuration file that has the error. > Kristin > > -----Original Message----- > From: Bill Ross [mailto:ross.cgl.ucsf.edu] > Sent: Wednesday, July 12, 2017 6:45 PM > To: amber.ambermd.org > Subject: Re: [AMBER] Problem with running mdout_analyzer.py > > Correction - not a broken install, but a broken config that is concatenating names instead of choosing one. > > Bill > > > On 7/12/17 3:43 PM, Bill Ross wrote: >> > /opt/anaconda1anaconda2anaconda3/lib/tcl8.5 >> >> That path sure looks like a broken install, but I don't know anything >> about anaconda. >> >> Bill >> >> On 7/12/17 3:40 PM, Krantzman, Kristin D wrote: >>> Greetings AMBER users, >>> I am trying to run mdout_analyzer.py and get the following error: >>> Traceback (most recent call last): >>> File "./mdout_analyzer.py", line 48, in <module> >>> root = Tk() >>> File "/usr/local/amber16/miniconda/lib/python2.7/lib-tk/Tkinter.py", line 1820, in __init__ >>> self.tk = _tkinter.create(screenName, baseName, className, >>> interactive, wantobjects, useTk, sync, use) >>> _tkinter.TclError: Can't find a usable init.tcl in the following directories: >>> /opt/anaconda1anaconda2anaconda3/lib/tcl8.5 >>> /usr/local/amber16/lib/tcl8.5 /usr/local/lib/tcl8.5 /usr/local/amber16/library /usr/local/library /usr/local/tcl8.5.18/library /usr/tcl8.5.18/library I reinstalled tcl, I still get this error. Could you help with this? >>> Best, Kristin >>> >>> >>> This probably means that Tcl wasn't installed properly. >>> Kristin D. Krantzman >>> Professor, Department of Chemistry and Biochemistry College of >>> Charleston Charleston, SC 29424 >>> (843) 953-3378 >>> >>> _______________________________________________ >>> AMBER mailing list >>> AMBER.ambermd.org >>> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org >>> _mailman_listinfo_amber&d=DwICAg&c=7MSSWy9Bs2yocjNQzurxOQ&r=rDr-VDoXC >>> Kpr5ouXXYSZkHF6q5gU19w8m7W8WZccZ7U&m=05GA69kYpADyAfYrZgotQ_jPUCJfvrw7 >>> ZdtuDC7nbNI&s=v8nAsRTANLujksAhkfYwDGyLppXkweYL1R6TmLUC-7w&e= >> _______________________________________________ >> AMBER mailing list >> AMBER.ambermd.org >> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org_ >> mailman_listinfo_amber&d=DwICAg&c=7MSSWy9Bs2yocjNQzurxOQ&r=rDr-VDoXCKp >> r5ouXXYSZkHF6q5gU19w8m7W8WZccZ7U&m=05GA69kYpADyAfYrZgotQ_jPUCJfvrw7Zdt >> uDC7nbNI&s=v8nAsRTANLujksAhkfYwDGyLppXkweYL1R6TmLUC-7w&e= > > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org_mailman_listinfo_amber&d=DwICAg&c=7MSSWy9Bs2yocjNQzurxOQ&r=rDr-VDoXCKpr5ouXXYSZkHF6q5gU19w8m7W8WZccZ7U&m=05GA69kYpADyAfYrZgotQ_jPUCJfvrw7ZdtuDC7nbNI&s=v8nAsRTANLujksAhkfYwDGyLppXkweYL1R6TmLUC-7w&e= > > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber ------------------------------ Message: 18 Date: Wed, 12 Jul 2017 23:06:01 +0000 From: Hai Nguyen <nhai.qn.gmail.com> Subject: Re: [AMBER] Problem with running mdout_analyzer.py To: AMBER Mailing List <amber.ambermd.org> Message-ID: <CAFNMPM9sDO5_OPZxt2cq7Y6UkUApUhqpaVc_WfsE74FnajojrA.mail.gmail.com> Content-Type: text/plain; charset="UTF-8" I think this was fixed in ambertools 17 http://archive.ambermd.org/201609/0415.html Can you upgrade? Hai On Wed, Jul 12, 2017 at 6:55 PM Krantzman, Kristin D <KrantzmanK.cofc.edu> wrote: > Hi Bill, > Python is automatically installed when I type "make install" with > AmberTools16. I do not know how to find the configuration file that has > the error. > Kristin > > -----Original Message----- > From: Bill Ross [mailto:ross.cgl.ucsf.edu] > Sent: Wednesday, July 12, 2017 6:45 PM > To: amber.ambermd.org > Subject: Re: [AMBER] Problem with running mdout_analyzer.py > > Correction - not a broken install, but a broken config that is > concatenating names instead of choosing one. > > Bill > > > On 7/12/17 3:43 PM, Bill Ross wrote: > > > /opt/anaconda1anaconda2anaconda3/lib/tcl8.5 > > > > That path sure looks like a broken install, but I don't know anything > > about anaconda. > > > > Bill > > > > On 7/12/17 3:40 PM, Krantzman, Kristin D wrote: > >> Greetings AMBER users, > >> I am trying to run mdout_analyzer.py and get the following error: > >> Traceback (most recent call last): > >> File "./mdout_analyzer.py", line 48, in <module> > >> root = Tk() > >> File > "/usr/local/amber16/miniconda/lib/python2.7/lib-tk/Tkinter.py", line 1820, > in __init__ > >> self.tk = _tkinter.create(screenName, baseName, className, > >> interactive, wantobjects, useTk, sync, use) > >> _tkinter.TclError: Can't find a usable init.tcl in the following > directories: > >> /opt/anaconda1anaconda2anaconda3/lib/tcl8.5 > >> /usr/local/amber16/lib/tcl8.5 /usr/local/lib/tcl8.5 > /usr/local/amber16/library /usr/local/library /usr/local/tcl8.5.18/library > /usr/tcl8.5.18/library I reinstalled tcl, I still get this error. Could > you help with this? > >> Best, Kristin > >> > >> > >> This probably means that Tcl wasn't installed properly. > >> Kristin D. Krantzman > >> Professor, Department of Chemistry and Biochemistry College of > >> Charleston Charleston, SC 29424 > >> (843) 953-3378 > >> > >> _______________________________________________ > >> AMBER mailing list > >> AMBER.ambermd.org > >> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org > >> _mailman_listinfo_amber&d=DwICAg&c=7MSSWy9Bs2yocjNQzurxOQ&r=rDr-VDoXC > >> Kpr5ouXXYSZkHF6q5gU19w8m7W8WZccZ7U&m=05GA69kYpADyAfYrZgotQ_jPUCJfvrw7 > >> ZdtuDC7nbNI&s=v8nAsRTANLujksAhkfYwDGyLppXkweYL1R6TmLUC-7w&e= > > > > _______________________________________________ > > AMBER mailing list > > AMBER.ambermd.org > > https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org_ > > mailman_listinfo_amber&d=DwICAg&c=7MSSWy9Bs2yocjNQzurxOQ&r=rDr-VDoXCKp > > r5ouXXYSZkHF6q5gU19w8m7W8WZccZ7U&m=05GA69kYpADyAfYrZgotQ_jPUCJfvrw7Zdt > > uDC7nbNI&s=v8nAsRTANLujksAhkfYwDGyLppXkweYL1R6TmLUC-7w&e= > > > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > > https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org_mailman_listinfo_amber&d=DwICAg&c=7MSSWy9Bs2yocjNQzurxOQ&r=rDr-VDoXCKpr5ouXXYSZkHF6q5gU19w8m7W8WZccZ7U&m=05GA69kYpADyAfYrZgotQ_jPUCJfvrw7ZdtuDC7nbNI&s=v8nAsRTANLujksAhkfYwDGyLppXkweYL1R6TmLUC-7w&e= > > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber > ------------------------------ Message: 19 Date: Wed, 12 Jul 2017 16:07:44 -0700 From: Bill Ross <ross.cgl.ucsf.edu> Subject: Re: [AMBER] Problem with running mdout_analyzer.py To: amber.ambermd.org Message-ID: <bfd285f3-ea01-a7fa-a7d3-af8c06a3a0c4.cgl.ucsf.edu> Content-Type: text/plain; charset=utf-8; format=flowed Looking deeper, that may not be the critical problem, since other places checked are more amber-specific: > /usr/local/amber16/lib/tcl8.5 /usr/local/amber16/library You could look in those places for more relevant clues. Noting you are using system dirs for your amber install, that raises the possibility that the user may forget to run with permissions during the install, so it might be incomplete. On 7/12/17 4:02 PM, Bill Ross wrote: > Hi Kristin, > > Try > > $ env > > and see if there are any clues. Probably a variable with a name > including LIB points there, and from that we may reason backwards from > general principles, absent expert help. > > Bill > > > On 7/12/17 3:55 PM, Krantzman, Kristin D wrote: >> Hi Bill, >> Python is automatically installed when I type "make install" with AmberTools16. I do not know how to find the configuration file that has the error. >> Kristin >> >> -----Original Message----- >> From: Bill Ross [mailto:ross.cgl.ucsf.edu] >> Sent: Wednesday, July 12, 2017 6:45 PM >> To: amber.ambermd.org >> Subject: Re: [AMBER] Problem with running mdout_analyzer.py >> >> Correction - not a broken install, but a broken config that is concatenating names instead of choosing one. >> >> Bill >> >> >> On 7/12/17 3:43 PM, Bill Ross wrote: >>> > /opt/anaconda1anaconda2anaconda3/lib/tcl8.5 >>> >>> That path sure looks like a broken install, but I don't know anything >>> about anaconda. >>> >>> Bill >>> >>> On 7/12/17 3:40 PM, Krantzman, Kristin D wrote: >>>> Greetings AMBER users, >>>> I am trying to run mdout_analyzer.py and get the following error: >>>> Traceback (most recent call last): >>>> File "./mdout_analyzer.py", line 48, in <module> >>>> root = Tk() >>>> File "/usr/local/amber16/miniconda/lib/python2.7/lib-tk/Tkinter.py", line 1820, in __init__ >>>> self.tk = _tkinter.create(screenName, baseName, className, >>>> interactive, wantobjects, useTk, sync, use) >>>> _tkinter.TclError: Can't find a usable init.tcl in the following directories: >>>> /opt/anaconda1anaconda2anaconda3/lib/tcl8.5 >>>> /usr/local/amber16/lib/tcl8.5 /usr/local/lib/tcl8.5 /usr/local/amber16/library /usr/local/library /usr/local/tcl8.5.18/library /usr/tcl8.5.18/library I reinstalled tcl, I still get this error. Could you help with this? >>>> Best, Kristin >>>> >>>> >>>> This probably means that Tcl wasn't installed properly. >>>> Kristin D. Krantzman >>>> Professor, Department of Chemistry and Biochemistry College of >>>> Charleston Charleston, SC 29424 >>>> (843) 953-3378 >>>> >>>> _______________________________________________ >>>> AMBER mailing list >>>> AMBER.ambermd.org >>>> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org >>>> _mailman_listinfo_amber&d=DwICAg&c=7MSSWy9Bs2yocjNQzurxOQ&r=rDr-VDoXC >>>> Kpr5ouXXYSZkHF6q5gU19w8m7W8WZccZ7U&m=05GA69kYpADyAfYrZgotQ_jPUCJfvrw7 >>>> ZdtuDC7nbNI&s=v8nAsRTANLujksAhkfYwDGyLppXkweYL1R6TmLUC-7w&e= >>> _______________________________________________ >>> AMBER mailing list >>> AMBER.ambermd.org >>> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org_ >>> mailman_listinfo_amber&d=DwICAg&c=7MSSWy9Bs2yocjNQzurxOQ&r=rDr-VDoXCKp >>> r5ouXXYSZkHF6q5gU19w8m7W8WZccZ7U&m=05GA69kYpADyAfYrZgotQ_jPUCJfvrw7Zdt >>> uDC7nbNI&s=v8nAsRTANLujksAhkfYwDGyLppXkweYL1R6TmLUC-7w&e= >> _______________________________________________ >> AMBER mailing list >> AMBER.ambermd.org >> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org_mailman_listinfo_amber&d=DwICAg&c=7MSSWy9Bs2yocjNQzurxOQ&r=rDr-VDoXCKpr5ouXXYSZkHF6q5gU19w8m7W8WZccZ7U&m=05GA69kYpADyAfYrZgotQ_jPUCJfvrw7ZdtuDC7nbNI&s=v8nAsRTANLujksAhkfYwDGyLppXkweYL1R6TmLUC-7w&e= >> >> _______________________________________________ >> AMBER mailing list >> AMBER.ambermd.org >> http://lists.ambermd.org/mailman/listinfo/amber > > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber ------------------------------ Message: 20 Date: Wed, 12 Jul 2017 23:18:58 +0000 From: "Krantzman, Kristin D" <KrantzmanK.cofc.edu> Subject: Re: [AMBER] Problem with running mdout_analyzer.py To: AMBER Mailing List <amber.ambermd.org> Message-ID: <CY1PR0401MB10663DE92093C80A848F6BA9B8AF0.CY1PR0401MB1066.namprd04.prod.outlook.com> Content-Type: text/plain; charset="us-ascii" Thank you, Hai and Bill! I will upgrade to Ambertools17. The export commands worked and I am able to run mdout_analyzer.py. Best, Kristin -----Original Message----- From: Hai Nguyen [mailto:nhai.qn.gmail.com] Sent: Wednesday, July 12, 2017 7:06 PM To: AMBER Mailing List <amber.ambermd.org> Subject: Re: [AMBER] Problem with running mdout_analyzer.py I think this was fixed in ambertools 17 https://urldefense.proofpoint.com/v2/url?u=http-3A__archive.ambermd.org_201609_0415.html&d=DwICAg&c=7MSSWy9Bs2yocjNQzurxOQ&r=rDr-VDoXCKpr5ouXXYSZkHF6q5gU19w8m7W8WZccZ7U&m=gNpmlp0JZCqzdGU58EMVL2si8D0Kc6_xDioU3yZA9SU&s=a-oXtjKpcuqsKTvqBus6PHqR1HdqS4HUfgFtg6KLedE&e= Can you upgrade? Hai On Wed, Jul 12, 2017 at 6:55 PM Krantzman, Kristin D <KrantzmanK.cofc.edu> wrote: > Hi Bill, > Python is automatically installed when I type "make install" with > AmberTools16. I do not know how to find the configuration file that > has the error. > Kristin > > -----Original Message----- > From: Bill Ross [mailto:ross.cgl.ucsf.edu] > Sent: Wednesday, July 12, 2017 6:45 PM > To: amber.ambermd.org > Subject: Re: [AMBER] Problem with running mdout_analyzer.py > > Correction - not a broken install, but a broken config that is > concatenating names instead of choosing one. > > Bill > > > On 7/12/17 3:43 PM, Bill Ross wrote: > > > /opt/anaconda1anaconda2anaconda3/lib/tcl8.5 > > > > That path sure looks like a broken install, but I don't know > > anything about anaconda. > > > > Bill > > > > On 7/12/17 3:40 PM, Krantzman, Kristin D wrote: > >> Greetings AMBER users, > >> I am trying to run mdout_analyzer.py and get the following error: > >> Traceback (most recent call last): > >> File "./mdout_analyzer.py", line 48, in <module> > >> root = Tk() > >> File > "/usr/local/amber16/miniconda/lib/python2.7/lib-tk/Tkinter.py", line > 1820, in __init__ > >> self.tk = _tkinter.create(screenName, baseName, className, > >> interactive, wantobjects, useTk, sync, use) > >> _tkinter.TclError: Can't find a usable init.tcl in the following > directories: > >> /opt/anaconda1anaconda2anaconda3/lib/tcl8.5 > >> /usr/local/amber16/lib/tcl8.5 /usr/local/lib/tcl8.5 > /usr/local/amber16/library /usr/local/library > /usr/local/tcl8.5.18/library /usr/tcl8.5.18/library I reinstalled tcl, > I still get this error. Could you help with this? > >> Best, Kristin > >> > >> > >> This probably means that Tcl wasn't installed properly. > >> Kristin D. Krantzman > >> Professor, Department of Chemistry and Biochemistry College of > >> Charleston Charleston, SC 29424 > >> (843) 953-3378 > >> > >> _______________________________________________ > >> AMBER mailing list > >> AMBER.ambermd.org > >> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.o > >> rg > >> _mailman_listinfo_amber&d=DwICAg&c=7MSSWy9Bs2yocjNQzurxOQ&r=rDr-VDo > >> XC > >> Kpr5ouXXYSZkHF6q5gU19w8m7W8WZccZ7U&m=05GA69kYpADyAfYrZgotQ_jPUCJfvr > >> w7 ZdtuDC7nbNI&s=v8nAsRTANLujksAhkfYwDGyLppXkweYL1R6TmLUC-7w&e= > > > > _______________________________________________ > > AMBER mailing list > > AMBER.ambermd.org > > https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.or > > g_ > > mailman_listinfo_amber&d=DwICAg&c=7MSSWy9Bs2yocjNQzurxOQ&r=rDr-VDoXC > > Kp > > r5ouXXYSZkHF6q5gU19w8m7W8WZccZ7U&m=05GA69kYpADyAfYrZgotQ_jPUCJfvrw7Z > > dt uDC7nbNI&s=v8nAsRTANLujksAhkfYwDGyLppXkweYL1R6TmLUC-7w&e= > > > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > > https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org_ > mailman_listinfo_amber&d=DwICAg&c=7MSSWy9Bs2yocjNQzurxOQ&r=rDr-VDoXCKp > r5ouXXYSZkHF6q5gU19w8m7W8WZccZ7U&m=05GA69kYpADyAfYrZgotQ_jPUCJfvrw7Zdt > uDC7nbNI&s=v8nAsRTANLujksAhkfYwDGyLppXkweYL1R6TmLUC-7w&e= > > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org_ > mailman_listinfo_amber&d=DwICAg&c=7MSSWy9Bs2yocjNQzurxOQ&r=rDr-VDoXCKp > r5ouXXYSZkHF6q5gU19w8m7W8WZccZ7U&m=gNpmlp0JZCqzdGU58EMVL2si8D0Kc6_xDio > U3yZA9SU&s=OJQOCPBuSUUEWEL3eMiwjdACU5x6jme_PeFsKwpnffA&e= > _______________________________________________ AMBER mailing list AMBER.ambermd.org https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org_mailman_listinfo_amber&d=DwICAg&c=7MSSWy9Bs2yocjNQzurxOQ&r=rDr-VDoXCKpr5ouXXYSZkHF6q5gU19w8m7W8WZccZ7U&m=gNpmlp0JZCqzdGU58EMVL2si8D0Kc6_xDioU3yZA9SU&s=OJQOCPBuSUUEWEL3eMiwjdACU5x6jme_PeFsKwpnffA&e= ------------------------------ Message: 21 Date: Wed, 12 Jul 2017 21:47:45 -0500 From: Aldo Segura Cabrera <aldoseguracabrera.gmail.com> Subject: [AMBER] MCPB.py issue To: amber.ambermd.org Message-ID: <CAM5gP6tUe3d7KdQ_cZT5ALPwUe4jViwU-7Hnm93JzViyoycLLA.mail.gmail.com> Content-Type: text/plain; charset="UTF-8" Hello Amber users, I?m following the Heme-Cys tutorial for MCPB.py I?m in the step 4 to get the mol2 files for the metal site (HM1.mol2, CM1.mol2, and FE1.mol2) by: MCPB.py -i 4ZF6.in -s 3 However, it didn?t work. I addition, I tried to fix this issue according to this post: http://archive.ambermd.org/201610/0448.html I obtained the same result. Here is the output of the command line: The input file you are using is : 4ZF6.in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The following is the input variable you have: The variable ion_ids is : [8551] The variable ion_info is : [] The variable ion_mol2files is : ['FE.mol2'] The variable original_pdb is : tebu_s_complex_H_renum.pdb The variable add_bonded_pairs is : [] The variable add_redcrd is : 0 The variable additional_resids is : [] The variable anglefc_avg is : 0 The variable bondfc_avg is : 0 The variable chgfix_resids is : [] The variable cut_off is : 2.8 The variable force_field is : ff14SB The variable frcmod_files is : ['HEM.frcmod'] The variable gaff is : 1 The variable group_name is : tebu_s_complex The variable ion_paraset is : CM (Only for nonbonded model) The variable large_opt is : 0 The variable lgmodel_chg is : -99 The variable lgmodel_spin is : -99 -99 means program will assign a charge automatically. The variable naa_mol2files is : ['HEM.mol2'] The variable scale_factor is : 1.0 ATTENTION: This is the scale factor of frequency. The force constants will be scaled by multiplying the square of scale_factor. The variable smmodel_chg is : -99 The variable smmodel_spin is : -99 -99 means program will assign a charge automatically. The variable software_version is : g09 The variable sqm_opt is : 0 The variable water_model is : TIP3P The variable xstru is : 0 ****************************************************************** * * *======================RESP Charge fitting=======================* * * ****************************************************************** ***Generating the 1st stage resp charge fitting input file... ***Generating the 2nd stage resp charge fitting input file... ***Doing the RESP charge fiting... Traceback (most recent call last): File "/home/my_home/software/amber16/bin/MCPB.py", line 684, in <module> premol2fs, mcresname, 1, chgfix_resids, g0x, lgchg) File "/home/my_home/software/amber16/lib/python2.7/site-packages/pymsmt/mcpb/resp_fitting.py", line 468, in resp_fitting chgs = read_resp_file('resp2.chg') File "/home/my_home/software/amber16/lib/python2.7/site-packages/pymsmt/mcpb/resp_fitting.py", line 24, in read_resp_file chgs.append(float(i)) ValueError: invalid literal for float(): 0.000000******************** Regards, Aldo ------------------------------ Message: 22 Date: Thu, 13 Jul 2017 06:18:51 +0000 (UTC) From: Saikat Pal <saikatpaliitg.yahoo.com> Subject: Re: [AMBER] Amber installation To: AMBER Mailing List <amber.ambermd.org> Message-ID: <1348737.5049180.1499926731949.mail.yahoo.com> Content-Type: text/plain; charset=UTF-8 Thank you sir for your reply. I have followed your opinion. make install this is the last part: running install_scripts copying build/scripts-2.7/pdb4amber -> /home/saikat/AMBER/amber-14/amber16//bin changing mode of /home/saikat/AMBER/amber-14/amber16//bin/pdb4amber to 775 running install_egg_info Writing /home/saikat/AMBER/amber-14/amber16//lib/python2.7/site-packages/pdb4amber-1.3-py2.7.egg-info /home/saikat/AMBER/amber-14/amber16//bin/amber.python fix_conda_fortran.py make[2]: Leaving directory '/home/saikat/AMBER/amber-14/amber16/AmberTools/src' Installation of AmberTools17 serial is complete at Thu Jul 13 11:19:47 IST 2017. make[1]: Leaving directory '/home/saikat/AMBER/amber-14/amber16/AmberTools/src' ============================================================== /home/saikat/AMBER/amber-14/amber16//src/Makefile not found, or -noamber was set. This is expected if you do not have Amber16. ============================================================== Now when I command "make test" this error is showing: make test (cd AmberTools/test && make test) make[1]: Entering directory '/home/saikat/AMBER/amber-14/amber16/AmberTools/test' ./test_at_serial.sh Error: Could not import Amber Python modules! ?? Probably your Amber Python environment was not set up correctly. We recommend adding the line: ?? test -f /home/saikat/AMBER/amber-14/amber16//amber.sh??&& source /home/saikat/AMBER/amber-14/amber16//amber.sh (sh/bash/zsh) or ?? test -f /home/saikat/AMBER/amber-14/amber16//amber.csh && source /home/saikat/AMBER/amber-14/amber16//amber.csh (csh/tcsh) to your login shell resource file (e.g., ~/.bashrc or ~/.cshrc). Makefile:8: recipe for target 'test' failed make[1]: *** [test] Error 1 make[1]: Leaving directory '/home/saikat/AMBER/amber-14/amber16/AmberTools/test' Makefile:61: recipe for target 'test.serial' failed make: *** [test.serial] Error 2 what should I do ??plz help me out. Thanks and regards, Saikat Pal On Wednesday 12 July 2017, 8:51:27 PM IST, Daniel Roe <daniel.r.roe.gmail.com> wrote: Use amber16, and source the amber.sh (or amber.csh) file that is created therein to set up your environment. The only thing from amber14 that isn't in AmberTools 17 is pmemd, and that does not require that AMBERHOME is set. -Dan On Wed, Jul 12, 2017 at 11:01 AM, Saikat Pal <saikatpaliitg.yahoo.com> wrote: > Dear all, > I want to install Amber 14 with AMBER 17 tools.When I untar AmberTools17.tar.bz2 it creates amber16 folder and Amber14.tar.bz2 it creates amber14 .There are 2 folders generated.Which one should I export for AMBERHOME?Plz help me out . > Thanks and regards > Saikat > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber -- ------------------------- Daniel R. Roe Laboratory of Computational Biology National Institutes of Health, NHLBI 5635 Fishers Ln, Rm T900 Rockville MD, 20852 https://www.lobos.nih.gov/lcb _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amber ------------------------------ Message: 23 Date: Thu, 13 Jul 2017 01:35:07 -0700 From: Bill Ross <ross.cgl.ucsf.edu> Subject: Re: [AMBER] Amber installation To: amber.ambermd.org Message-ID: <ef77c39c-b277-f4fe-2276-248fc18c2605.cgl.ucsf.edu> Content-Type: text/plain; charset=utf-8; format=flowed On 7/12/17 11:18 PM, Saikat Pal wrote: > We recommend adding the line: > > test -f /home/saikat/AMBER/amber-14/amber16//amber.sh && source /home/saikat/AMBER/amber-14/amber16//amber.sh (sh/bash/zsh) > or > test -f /home/saikat/AMBER/amber-14/amber16//amber.csh && source /home/saikat/AMBER/amber-14/amber16//amber.csh (csh/tcsh) > > to your login shell resource file (e.g., ~/.bashrc or ~/.cshrc). ------------------------------ Message: 24 Date: Thu, 13 Jul 2017 09:03:31 +0000 From: Lizelle Lubbe <LBBLIZ002.myuct.ac.za> Subject: Re: [AMBER] parmed validity off-diagonal LJ parameters To: AMBER Mailing List <amber.ambermd.org> Message-ID: <DB3PR03MB09860E05B1BD816D03780DDEB4AC0.DB3PR03MB0986.eurprd03.prod.outlook.com> Content-Type: text/plain; charset="us-ascii" Hi Daniel, Thanks for the helpful reply - it makes more sense now. I've had a look at the prmtop manual describing the different flags but I am still stuck. If I haven't modified any LJ parameters willingly (and therefore don't know the atom type for which there are more than 1 set of LJ parameters), how would I be able to fix this? Kind regards Lizelle Lubbe PhD (Medical biochemistry) candidate Department of Integrative Biomedical Sciences University of Cape Town ________________________________________ From: Daniel Roe <daniel.r.roe.gmail.com> Sent: 12 July 2017 03:30:05 PM To: AMBER Mailing List Subject: Re: [AMBER] parmed validity off-diagonal LJ parameters Hi, "Modified off-diagonal LJ parameters" means an atom type has more than one set of LJ parameters associated with it. Normally each atom type has one set of LJ parameters (energy well depth and sigma) which are combined with the parameters from another type in order to obtain the A and B parameters used in the common form of the 6-12 potential term. So given 3 atom types A, B, and C you have: AA AB AC BB BC CC It's simple to envision this as a symmetric half matrix (although harder to display with a non-fixed-width font): AA AB BB AC BC CC If you know the combining rules used, you can back-calculate the original LJ params from the self (diagonal) terms. One school of thought is that in some cases, these LJ parameters need to be adjusted between different atom types; essentially saying something like "A" should look different to "B" than it does to "C". So you might have 'A' parameters for 'AA' and 'AC', but 'a' parameters for 'B': AA aB BB AC BC CC The 'aB' term is a modified off-diagonal LJ term. TL;DR: I'm not sure how MCPB.py assigns parameters, but it's possible that it does create some off-diagonal LJ modifications. Hopefully an MCPB.py developer can comment on this. -Dan On Wed, Jul 12, 2017 at 8:23 AM, Lizelle Lubbe <LBBLIZ002.myuct.ac.za> wrote: > Hi all, > > I have searched online for a solution to this problem but found nothing yet. Any suggestions?? > > I've done some digging and saw that the frcmod file generated by MCPB.py gives the following Lennard Jones parameters (X1-X4 are the 4 coordinating ligands and Z1 the zinc ion) > > NONB > X1 1.8240 0.1700 OPLS > X2 1.8240 0.1700 OPLS > X3 1.6612 0.2100 OPLS > X4 1.7683 0.1520 TIP3P water model > Z1 1.395 0.0149170000 IOD set from Li et al. JCTC, 2013, 9, 2733 > > This is identical to that given in the tutorial example's frcmod file. > > Using parmed to check the zinc ion in my prmtop gives: > ATOM RES RESNAME NAME TYPE LJ Radius LJ Depth Mass Charge GB Radius GB Screen > 9749 613 ZN1 ZN Z1 1.3950 0.0149 65.4000 1.4993 1.5000 0.8000 > >> printLJTypes .ZN > > ATOM NUMBER NAME TYPE > --------------------------------------------- > ATOM 9749 ZN Z1 : Type index: 15 > >> checkValidity > Determining validity of prmtop > 1 total warnings > > NonUniversalWarning: Modified off-diagonal LJ parameters detected > > The tutorial's prmtop gives essentially the same (except for charge) > ATOM RES RESNAME NAME TYPE LJ Radius LJ Depth Mass Charge GB Radius GB Screen > 4018 256 ZN1 ZN M1 1.3950 0.0149 65.4000 0.4335 1.5000 0.8000 > >> printLJTypes .ZN > > ATOM NUMBER NAME TYPE > --------------------------------------------- > ATOM 4018 ZN M1 : Type index: 15 > >> checkValidity > Determining validity of prmtop > 1OKL_solv.prmtop looks OK to me! > > This time there is no warning message so I guess it has nothing to do with using newly derived parameters as I previously thought. > Given that I never changed any LJ parameters in parmed, shouldn't the matrix be correctly written from the forcefield information? > > Does anyone have a suggestion as to the source of this warning and how to solve it? > > Kind regards > > Lizelle Lubbe > > PhD (Medical biochemistry) candidate > Department of Integrative Biomedical Sciences > University of Cape Town > ________________________________________ > From: Lizelle Lubbe > Sent: 11 July 2017 05:00:59 PM > To: amber.ambermd.org > Subject: parmed validity off-diagonal LJ parameters > > Dear Amber users, > > I want to simulate a zinc metalloprotease and have determined the metal site parameters using MCPB.py > After tleap I ran the prmtop through cpptraj and got the following error: > > Error: Atom 12495 was assigned a lower molecule # than previous atom. This can > Error: happen if 1) bond information is incorrect or missing, or 2) if the > Error: atom numbering in molecules is not sequential. If topology did not > Error: originally contain bond info, 1) can potentially be fixed by > Error: increasing the bondsearch cutoff offset (currently 0.200). 2) can be > Error: fixed by either using the 'fixatomorder' command, or using > Error: the 'setMolecules' command in parmed.py. > Error: Could not determine molecule information for editnoLINK_bondhash_CLedit_NDOM_CPLX_Neut_Sol.prmtop. > Error: SetSolventInfo: No molecule information. > Error: Could not determine solvent information for editnoLINK_bondhash_CLedit_NDOM_CPLX_Neut_Sol.prmtop. > > Using setMolecules in parmed.py gave a new prmtop with no errors in cpptraj. > > Running parmed and checkValidity on the new prmtop gave the following warning: >> checkValidity > Determining validity of prmtop > 1 total warnings > NonUniversalWarning: Modified off-diagonal LJ parameters detected > > I have not changed the LJ parameters in parmed. > > Jason Swails mentioned in a previous post (Curious behavior of cpptraj in ambertools 13.1): >> Hmm... I wonder why this warning was triggered. Unless you used "changeLJPair" in ParmEd (or somehow otherwise manually changed the LENNARD_JONES_ACOEF or BCOEF elements of the topology file, this should not be an issue. > > I noticed that the previous post was also about a protein coordinated to zinc. Does the new parameters derived from mcpb.py somehow trigger this warning? > Should I worry about it or can I use the prmtop and rst7 for minimization? > > Kind regards > > Lizelle Lubbe > > PhD (Medical biochemistry) candidate > Department of Integrative Biomedical Sciences > University of Cape Town > Disclaimer - University of Cape Town This e-mail is subject to UCT policies and e-mail disclaimer published on our website at http://www.uct.ac.za/about/policies/emaildisclaimer/ or obtainable from +27 21 650 9111. If this e-mail is not related to the business of UCT, it is sent by the sender in an individual capacity. Please report security incidents or abuse via csirt.uct.ac.za > > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber -- ------------------------- Daniel R. Roe Laboratory of Computational Biology National Institutes of Health, NHLBI 5635 Fishers Ln, Rm T900 Rockville MD, 20852 https://www.lobos.nih.gov/lcb _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amber Disclaimer - University of Cape Town This e-mail is subject to UCT policies and e-mail disclaimer published on our website at http://www.uct.ac.za/about/policies/emaildisclaimer/ or obtainable from +27 21 650 9111. If this e-mail is not related to the business of UCT, it is sent by the sender in an individual capacity. Please report security incidents or abuse via csirt.uct.ac.za ------------------------------ Message: 25 Date: Thu, 13 Jul 2017 09:15:28 +0000 From: Michael Shokhen <michael.shokhen.biu.ac.il> Subject: [AMBER] antechamber problem To: "AMBER.ambermd.org" <AMBER.ambermd.org> Message-ID: <AM5PR04MB32839BC1FD6CF2EB6A2527F2B6AC0.AM5PR04MB3283.eurprd04.prod.outlook.com> Content-Type: text/plain; charset="iso-8859-1" Dear Amber experts, I have on my server AMBER16 and AMBER TOOLS16. The ligand MS75 in my protein-ligand complex needs previous parametrisation by ANTECHAMBER. The MS75 ligand has a total charge -1. Applying original MOPAC2016 with AM1 hamiltonian I have calculated the MS75 without any problem. Unfortunately, the standard AMBER command line: antechamber -i MS75.pdb -fi pdb -o MS75.mol2 -fo mol2 -c bcc -s 2 returns with error message because the input MS75.pdb was incorrectly interpreted as having charge=0 Running: /var/spool/scratch/shokhen/amber16/bin/bondtype -j full -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac Running: /var/spool/scratch/shokhen/amber16/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff Total number of electrons: 231; net charge: 0 INFO: Number of electrons is odd: 231 Please check the total charge (-nc flag) and spin multiplicity (-m flag) Running: /var/spool/scratch/shokhen/amber16/bin/sqm -O -i sqm.in -o sqm.out Error: cannot run "/var/spool/scratch/shokhen/amber16/bin/sqm -O -i sqm.in -o sqm.out" of bcc() in charge.c properly, exit The top of smq.in file automatically generated by bcc parameter in the antechamber command line demonstrates incorrect molecular charge definition based on input coordinates of the MS75.pdb: Run semi-empirical minimization &qmmm qm_theory='AM1', grms_tol=0.0005, scfconv=1.d-10, qmcharge=0, Could somebody advise me how to modify the command line antechamber -i MS75.pdb -fi pdb -o MS75.mol2 -fo mol2 -c bcc -s 2 in order to setup the charge=-1 for MS75 ligand? Thank you, Michael ------------------------------ Message: 26 Date: Thu, 13 Jul 2017 15:12:44 +0530 From: Prayagraj Fandilolu <fprayagraj.gmail.com> Subject: Re: [AMBER] antechamber problem To: AMBER Mailing List <amber.ambermd.org> Message-ID: <CAFDrOJhVysCqxhASBViX+eJ-WoxdaCtPiFH2_fZ6oskqdxeMwg.mail.gmail.com> Content-Type: text/plain; charset="UTF-8" Dear Michael, Kindly note the information given during running the job Running: /var/spool/scratch/shokhen/amber16/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff Total number of electrons: 231; net charge: 0 INFO: Number of electrons is odd: 231 Please check the total charge (-nc flag) and spin multiplicity (-m flag) you can adjust the charge and multiplicity of your molecule by putting the -nc and -m flags respectively to your command. As your molecule has a charge of -1, you can specify it in the command as: antechamber -i MS75.pdb -fi pdb -o MS75.mol2 -fo mol2 -c bcc -s 2 -nc -1 (-m 0) This should solve your problem... All the best!!! Prayagraj Fandilolu Research Scholar, Structural Bioinformatics Unit Department of Biochemistry Shivaji University, Kolhapur - 416004 (MS) India On Thu, Jul 13, 2017 at 2:45 PM, Michael Shokhen <michael.shokhen.biu.ac.il> wrote: > Dear Amber experts, > > > I have on my server AMBER16 and AMBER TOOLS16. > > The ligand MS75 in my protein-ligand complex needs previous > parametrisation by ANTECHAMBER. > > The MS75 ligand has a total charge -1. > > Applying original MOPAC2016 with AM1 hamiltonian I have calculated the MS75 > > without any problem. > > Unfortunately, the standard AMBER command line: > > > antechamber -i MS75.pdb -fi pdb -o MS75.mol2 -fo mol2 -c bcc -s 2 > > returns with error message because the input MS75.pdb was incorrectly > interpreted as having charge=0 > > Running: /var/spool/scratch/shokhen/amber16/bin/bondtype -j full -i > ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac > > Running: /var/spool/scratch/shokhen/amber16/bin/atomtype -i > ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff > Total number of electrons: 231; net charge: 0 > INFO: Number of electrons is odd: 231 > Please check the total charge (-nc flag) and spin multiplicity (-m > flag) > > Running: /var/spool/scratch/shokhen/amber16/bin/sqm -O -i sqm.in -o > sqm.out > Error: cannot run "/var/spool/scratch/shokhen/amber16/bin/sqm -O -i sqm.in > -o sqm.out" of bcc() in charge.c properly, exit > > > > The top of smq.in file automatically generated by bcc parameter in the > antechamber command line > demonstrates incorrect molecular charge definition based on input > coordinates of the MS75.pdb: > > Run semi-empirical minimization > &qmmm > qm_theory='AM1', grms_tol=0.0005, > scfconv=1.d-10, qmcharge=0, > > > Could somebody advise me how to modify the command line > > antechamber -i MS75.pdb -fi pdb -o MS75.mol2 -fo mol2 -c bcc -s 2 > > > in order to setup the charge=-1 for MS75 ligand? > > > Thank you, > > Michael > > > > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber > ------------------------------ Message: 27 Date: Thu, 13 Jul 2017 10:22:32 +0000 From: Michael Shokhen <michael.shokhen.biu.ac.il> Subject: Re: [AMBER] antechamber problem To: AMBER Mailing List <AMBER.ambermd.org> Message-ID: <AM5PR04MB3283F2691DF6FFC163FD9C42B6AC0.AM5PR04MB3283.eurprd04.prod.outlook.com> Content-Type: text/plain; charset="us-ascii" Dear Prayagraj Fandilolu, Thank you for your advise. Now command works correct. All the best, Michael ***************************** Michael Shokhen, PhD Associate Professor Department of Chemistry Bar Ilan University, Ramat Gan, 52900 Israel email: shokhen.mail.biu.ac.il<https://webmail.biu.ac.il/owa/redir.aspx?C=a160ef9b9a6b4d06992402715d3ee465&URL=mailto%3ashokhen%40mail.biu.ac.il> ________________________________ From: Prayagraj Fandilolu <fprayagraj.gmail.com> Sent: Thursday, July 13, 2017 12:42:44 PM To: AMBER Mailing List Subject: Re: [AMBER] antechamber problem Dear Michael, Kindly note the information given during running the job Running: /var/spool/scratch/shokhen/amber16/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff Total number of electrons: 231; net charge: 0 INFO: Number of electrons is odd: 231 Please check the total charge (-nc flag) and spin multiplicity (-m flag) you can adjust the charge and multiplicity of your molecule by putting the -nc and -m flags respectively to your command. As your molecule has a charge of -1, you can specify it in the command as: antechamber -i MS75.pdb -fi pdb -o MS75.mol2 -fo mol2 -c bcc -s 2 -nc -1 (-m 0) This should solve your problem... All the best!!! Prayagraj Fandilolu Research Scholar, Structural Bioinformatics Unit Department of Biochemistry Shivaji University, Kolhapur - 416004 (MS) India On Thu, Jul 13, 2017 at 2:45 PM, Michael Shokhen <michael.shokhen.biu.ac.il> wrote: > Dear Amber experts, > > > I have on my server AMBER16 and AMBER TOOLS16. > > The ligand MS75 in my protein-ligand complex needs previous > parametrisation by ANTECHAMBER. > > The MS75 ligand has a total charge -1. > > Applying original MOPAC2016 with AM1 hamiltonian I have calculated the MS75 > > without any problem. > > Unfortunately, the standard AMBER command line: > > > antechamber -i MS75.pdb -fi pdb -o MS75.mol2 -fo mol2 -c bcc -s 2 > > returns with error message because the input MS75.pdb was incorrectly > interpreted as having charge=0 > > Running: /var/spool/scratch/shokhen/amber16/bin/bondtype -j full -i > ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac > > Running: /var/spool/scratch/shokhen/amber16/bin/atomtype -i > ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff > Total number of electrons: 231; net charge: 0 > INFO: Number of electrons is odd: 231 > Please check the total charge (-nc flag) and spin multiplicity (-m > flag) > > Running: /var/spool/scratch/shokhen/amber16/bin/sqm -O -i sqm.in -o > sqm.out > Error: cannot run "/var/spool/scratch/shokhen/amber16/bin/sqm -O -i sqm.in > -o sqm.out" of bcc() in charge.c properly, exit > > > > The top of smq.in file automatically generated by bcc parameter in the > antechamber command line > demonstrates incorrect molecular charge definition based on input > coordinates of the MS75.pdb: > > Run semi-empirical minimization > &qmmm > qm_theory='AM1', grms_tol=0.0005, > scfconv=1.d-10, qmcharge=0, > > > Could somebody advise me how to modify the command line > > antechamber -i MS75.pdb -fi pdb -o MS75.mol2 -fo mol2 -c bcc -s 2 > > > in order to setup the charge=-1 for MS75 ligand? > > > Thank you, > > Michael > > > > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber > _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amber ------------------------------ Message: 28 Date: Thu, 13 Jul 2017 10:58:08 +0000 From: Lizelle Lubbe <LBBLIZ002.myuct.ac.za> Subject: Re: [AMBER] parmed validity off-diagonal LJ parameters To: AMBER Mailing List <amber.ambermd.org>, Daniel Roe <daniel.r.roe.gmail.com> Message-ID: <DB3PR03MB0986B29CA6852DB36B6DC37CB4AC0.DB3PR03MB0986.eurprd03.prod.outlook.com> Content-Type: text/plain; charset="iso-8859-1" Hi, I've now loaded the prmtop into parmed and used printLJTypes to get an output of the atom types in the 23 LJ Index types. I then manually inspected each Index type in the list to see if some atoms within a particular index type have differing LJ parameters eg. printDetails .%C,C0,CA,C*,CW Atoms in each of these indices have identical LJ parameters. I could not detect a second set of parameters for any of the atom types. Here is the output: LJ Type IndexAtom type LJ radiusLJ depth 1 N3, N, Ng, X2, X11.82400.1700 2 H 0.60000.0157 3 CX, 2C, 3C, CT, Cg1.90800.1094 4 HP 1.10000.0157 5 HC 1.48700.0157 6 C, C0, CA, C*, CW1.90800.0860 7 O, O2 1.66120.2100 8 H1 1.38700.0157 9 HA 1.45900.0150 10 Oh, OH 1.72100.2104 11 HO 0.00000.0000 12 H4 1.40900.0150 13 H5 1.35900.0150 14 S 2.00000.2500 15 H2 1.28700.0157 16 Os, Oy 1.68370.1700 17 Ho 0.20000.0300 18 Z1 (ZN) 1.39500.0149 19 Cl- 2.25200.6029 20 X4 (WT1 O) 1.76830.1520 21 HW (WT1 TIP3P H)0.00000.0000 22 Na+ 1.47500.0317 23 OW (TIP3P O) 1.76830.1520 Could this perhaps mean that I don't have to worry about this warning and that the downstream programs will all work properly? Or is there another way in which I can try to find the source of error? Kind regards Lizelle Lubbe PhD (Medical biochemistry) candidate Department of Integrative Biomedical Sciences University of Cape Town ________________________________________ From: Lizelle Lubbe Sent: 13 July 2017 11:03 AM To: AMBER Mailing List Subject: Re: [AMBER] parmed validity off-diagonal LJ parameters Hi Daniel, Thanks for the helpful reply - it makes more sense now. I've had a look at the prmtop manual describing the different flags but I am still stuck. If I haven't modified any LJ parameters willingly (and therefore don't know the atom type for which there are more than 1 set of LJ parameters), how would I be able to fix this? Kind regards Lizelle Lubbe PhD (Medical biochemistry) candidate Department of Integrative Biomedical Sciences University of Cape Town ________________________________________ From: Daniel Roe <daniel.r.roe.gmail.com> Sent: 12 July 2017 03:30:05 PM To: AMBER Mailing List Subject: Re: [AMBER] parmed validity off-diagonal LJ parameters Hi, "Modified off-diagonal LJ parameters" means an atom type has more than one set of LJ parameters associated with it. Normally each atom type has one set of LJ parameters (energy well depth and sigma) which are combined with the parameters from another type in order to obtain the A and B parameters used in the common form of the 6-12 potential term. So given 3 atom types A, B, and C you have: AA AB AC BB BC CC It's simple to envision this as a symmetric half matrix (although harder to display with a non-fixed-width font): AA AB BB AC BC CC If you know the combining rules used, you can back-calculate the original LJ params from the self (diagonal) terms. One school of thought is that in some cases, these LJ parameters need to be adjusted between different atom types; essentially saying something like "A" should look different to "B" than it does to "C". So you might have 'A' parameters for 'AA' and 'AC', but 'a' parameters for 'B': AA aB BB AC BC CC The 'aB' term is a modified off-diagonal LJ term. TL;DR: I'm not sure how MCPB.py assigns parameters, but it's possible that it does create some off-diagonal LJ modifications. Hopefully an MCPB.py developer can comment on this. -Dan On Wed, Jul 12, 2017 at 8:23 AM, Lizelle Lubbe <LBBLIZ002.myuct.ac.za> wrote: > Hi all, > > I have searched online for a solution to this problem but found nothing yet. Any suggestions?? > > I've done some digging and saw that the frcmod file generated by MCPB.py gives the following Lennard Jones parameters (X1-X4 are the 4 coordinating ligands and Z1 the zinc ion) > > NONB > X1 1.8240 0.1700 OPLS > X2 1.8240 0.1700 OPLS > X3 1.6612 0.2100 OPLS > X4 1.7683 0.1520 TIP3P water model > Z1 1.395 0.0149170000 IOD set from Li et al. JCTC, 2013, 9, 2733 > > This is identical to that given in the tutorial example's frcmod file. > > Using parmed to check the zinc ion in my prmtop gives: > ATOM RES RESNAME NAME TYPE LJ Radius LJ Depth Mass Charge GB Radius GB Screen > 9749 613 ZN1 ZN Z1 1.3950 0.0149 65.4000 1.4993 1.5000 0.8000 > >> printLJTypes .ZN > > ATOM NUMBER NAME TYPE > --------------------------------------------- > ATOM 9749 ZN Z1 : Type index: 15 > >> checkValidity > Determining validity of prmtop > 1 total warnings > > NonUniversalWarning: Modified off-diagonal LJ parameters detected > > The tutorial's prmtop gives essentially the same (except for charge) > ATOM RES RESNAME NAME TYPE LJ Radius LJ Depth Mass Charge GB Radius GB Screen > 4018 256 ZN1 ZN M1 1.3950 0.0149 65.4000 0.4335 1.5000 0.8000 > >> printLJTypes .ZN > > ATOM NUMBER NAME TYPE > --------------------------------------------- > ATOM 4018 ZN M1 : Type index: 15 > >> checkValidity > Determining validity of prmtop > 1OKL_solv.prmtop looks OK to me! > > This time there is no warning message so I guess it has nothing to do with using newly derived parameters as I previously thought. > Given that I never changed any LJ parameters in parmed, shouldn't the matrix be correctly written from the forcefield information? > > Does anyone have a suggestion as to the source of this warning and how to solve it? > > Kind regards > > Lizelle Lubbe > > PhD (Medical biochemistry) candidate > Department of Integrative Biomedical Sciences > University of Cape Town > ________________________________________ > From: Lizelle Lubbe > Sent: 11 July 2017 05:00:59 PM > To: amber.ambermd.org > Subject: parmed validity off-diagonal LJ parameters > > Dear Amber users, > > I want to simulate a zinc metalloprotease and have determined the metal site parameters using MCPB.py > After tleap I ran the prmtop through cpptraj and got the following error: > > Error: Atom 12495 was assigned a lower molecule # than previous atom. This can > Error: happen if 1) bond information is incorrect or missing, or 2) if the > Error: atom numbering in molecules is not sequential. If topology did not > Error: originally contain bond info, 1) can potentially be fixed by > Error: increasing the bondsearch cutoff offset (currently 0.200). 2) can be > Error: fixed by either using the 'fixatomorder' command, or using > Error: the 'setMolecules' command in parmed.py. > Error: Could not determine molecule information for editnoLINK_bondhash_CLedit_NDOM_CPLX_Neut_Sol.prmtop. > Error: SetSolventInfo: No molecule information. > Error: Could not determine solvent information for editnoLINK_bondhash_CLedit_NDOM_CPLX_Neut_Sol.prmtop. > > Using setMolecules in parmed.py gave a new prmtop with no errors in cpptraj. > > Running parmed and checkValidity on the new prmtop gave the following warning: >> checkValidity > Determining validity of prmtop > 1 total warnings > NonUniversalWarning: Modified off-diagonal LJ parameters detected > > I have not changed the LJ parameters in parmed. > > Jason Swails mentioned in a previous post (Curious behavior of cpptraj in ambertools 13.1): >> Hmm... I wonder why this warning was triggered. Unless you used "changeLJPair" in ParmEd (or somehow otherwise manually changed the LENNARD_JONES_ACOEF or BCOEF elements of the topology file, this should not be an issue. > > I noticed that the previous post was also about a protein coordinated to zinc. Does the new parameters derived from mcpb.py somehow trigger this warning? > Should I worry about it or can I use the prmtop and rst7 for minimization? > > Kind regards > > Lizelle Lubbe > > PhD (Medical biochemistry) candidate > Department of Integrative Biomedical Sciences > University of Cape Town > Disclaimer - University of Cape Town This e-mail is subject to UCT policies and e-mail disclaimer published on our website at http://www.uct.ac.za/about/policies/emaildisclaimer/ or obtainable from +27 21 650 9111. If this e-mail is not related to the business of UCT, it is sent by the sender in an individual capacity. Please report security incidents or abuse via csirt.uct.ac.za > > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber -- ------------------------- Daniel R. Roe Laboratory of Computational Biology National Institutes of Health, NHLBI 5635 Fishers Ln, Rm T900 Rockville MD, 20852 https://www.lobos.nih.gov/lcb _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amber Disclaimer - University of Cape Town This e-mail is subject to UCT policies and e-mail disclaimer published on our website at http://www.uct.ac.za/about/policies/emaildisclaimer/ or obtainable from +27 21 650 9111. If this e-mail is not related to the business of UCT, it is sent by the sender in an individual capacity. Please report security incidents or abuse via csirt.uct.ac.za ------------------------------ Message: 29 Date: Thu, 13 Jul 2017 11:08:17 +0000 (UTC) From: Saikat Pal <saikatpaliitg.yahoo.com> Subject: Re: [AMBER] Amber installation To: AMBER Mailing List <amber.ambermd.org> Message-ID: <1807321277.5402567.1499944097057.mail.yahoo.com> Content-Type: text/plain; charset=UTF-8 I have added test -f /home/saikat/AMBER/amber-14/amber16//amber.sh? && source /home/saikat/AMBER/amber-14/amber16//amber.sh (sh/bash/zsh) in the .bashrc file but same error have shown. What should I do? Actually I want to analyse using AMBERTOOLS 17 for cpptraj.I have AMBERTOOLS 17 And AMBER 14 .please help me out . Thanks and regards, Saikat On Thursday 13 July 2017, 2:05:22 PM IST, Bill Ross <ross.cgl.ucsf.edu> wrote: On 7/12/17 11:18 PM, Saikat Pal wrote: > We recommend adding the line: > >? ? test -f /home/saikat/AMBER/amber-14/amber16//amber.sh? && source /home/saikat/AMBER/amber-14/amber16//amber.sh (sh/bash/zsh) > or >? ? test -f /home/saikat/AMBER/amber-14/amber16//amber.csh && source /home/saikat/AMBER/amber-14/amber16//amber.csh (csh/tcsh) > > to your login shell resource file (e.g., ~/.bashrc or ~/.cshrc). _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amber ------------------------------ Message: 30 Date: Thu, 13 Jul 2017 14:40:29 +0300 From: ARMIN HODAEI <ahodaei15.ku.edu.tr> Subject: [AMBER] prepin file for CMP ligand To: amber.ambermd.org Message-ID: <CAE-mGxy6FOvtB7RkbMxOKK9sbqQvp8omGbapBPzfWzM7M99oug.mail.gmail.com> Content-Type: text/plain; charset="UTF-8" Dear AMBER users, Do you know how can I define CMP ligands in xLEAP? I know that the procedure is to create a prepin file in ANTECHAMBER, but I have no idea where to start. Has anyone done this before? Sincerely, -- Armin Hodaei Department of Physics, Faculty of Arts and Sciences Koc University, Istanbul ------------------------------ Message: 31 Date: Thu, 13 Jul 2017 08:04:44 -0400 From: Daniel Roe <daniel.r.roe.gmail.com> Subject: Re: [AMBER] Amber installation To: AMBER Mailing List <amber.ambermd.org> Message-ID: <CAAC0qOZDnJh6Rsh-qs=EFFAOFvbWePZxHXO70x6eM8Jeys2BcQ.mail.gmail.com> Content-Type: text/plain; charset="UTF-8" On Thu, Jul 13, 2017 at 2:18 AM, Saikat Pal <saikatpaliitg.yahoo.com> wrote: > make[2]: Leaving directory '/home/saikat/AMBER/amber-14/amber16/AmberTools/src' > > Installation of AmberTools17 serial is complete at Thu Jul 13 11:19:47 IST 2017. > > make[1]: Leaving directory '/home/saikat/AMBER/amber-14/amber16/AmberTools/src' > ============================================================== > /home/saikat/AMBER/amber-14/amber16//src/Makefile not found, or -noamber was set. > This is expected if you do not have Amber16. > ============================================================== As the message states, AmberTools 17 installed just fine. The last message is just letting you know that you don't have Amber 16, so all is well. > Error: Could not import Amber Python modules! > Probably your Amber Python environment was not set up correctly. > > We recommend adding the line: > > test -f /home/saikat/AMBER/amber-14/amber16//amber.sh && source /home/saikat/AMBER/amber-14/amber16//amber.sh (sh/bash/zsh) > or > test -f /home/saikat/AMBER/amber-14/amber16//amber.csh && source /home/saikat/AMBER/amber-14/amber16//amber.csh (csh/tcsh) > > to your login shell resource file (e.g., ~/.bashrc or ~/.cshrc). This message is about as clear as error messages get. You need to 'source /home/saikat/AMBER/amber-14/amber16//amber.sh' (or the .csh version if you have C shell). -Dan > Makefile:8: recipe for target 'test' failed > make[1]: *** [test] Error 1 > make[1]: Leaving directory '/home/saikat/AMBER/amber-14/amber16/AmberTools/test' > Makefile:61: recipe for target 'test.serial' failed > make: *** [test.serial] Error 2 > > > > what should I do ??plz help me out. > Thanks and regards, > Saikat Pal > On Wednesday 12 July 2017, 8:51:27 PM IST, Daniel Roe <daniel.r.roe.gmail.com> wrote: > > Use amber16, and source the amber.sh (or amber.csh) file that is > created therein to set up your environment. The only thing from > amber14 that isn't in AmberTools 17 is pmemd, and that does not > require that AMBERHOME is set. > > -Dan > > On Wed, Jul 12, 2017 at 11:01 AM, Saikat Pal <saikatpaliitg.yahoo.com> wrote: >> Dear all, >> I want to install Amber 14 with AMBER 17 tools.When I untar AmberTools17.tar.bz2 it creates amber16 folder and Amber14.tar.bz2 it creates amber14 .There are 2 folders generated.Which one should I export for AMBERHOME?Plz help me out . >> Thanks and regards >> Saikat >> _______________________________________________ >> AMBER mailing list >> AMBER.ambermd.org >> http://lists.ambermd.org/mailman/listinfo/amber > > > > -- > ------------------------- > Daniel R. Roe > Laboratory of Computational Biology > National Institutes of Health, NHLBI > 5635 Fishers Ln, Rm T900 > Rockville MD, 20852 > https://www.lobos.nih.gov/lcb > > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber -- ------------------------- Daniel R. Roe Laboratory of Computational Biology National Institutes of Health, NHLBI 5635 Fishers Ln, Rm T900 Rockville MD, 20852 https://www.lobos.nih.gov/lcb ------------------------------ Message: 32 Date: Thu, 13 Jul 2017 17:55:37 +0530 From: Prayagraj Fandilolu <fprayagraj.gmail.com> Subject: Re: [AMBER] prepin file for CMP ligand To: AMBER Mailing List <amber.ambermd.org> Message-ID: <CAFDrOJhD4RMb4XvmD16=yqw3b44sbD1kAYSmeLYf1ruOXBqNog.mail.gmail.com> Content-Type: text/plain; charset="UTF-8" Hello Armin, In order to prepare a .prepin file you first need a proper 3D structure (.pdb) of your ligand. Then you should derive partial charges (RESP) charges for the atoms of your pdb. These charges can be derived by using Gaussian09 or RESP server or simply you can assign partial charges by using antechamber. You can google about Gaussian or RESP server (RED server). In antechamber, you can assign the partial charges by MOPAC or sqm . ## antechamber -i abc.pdb -fi pdb -o abc.mol2 -fo mol2 -c bcc -s 2 the output of this (a .mol2 file) will be carrying information about the assigned charges. You need to submit this file for generation of the prepin file for using in xLeap. ## antechamber -i abc.mol2 -fi mol2 -o abc.prepin -fo prepi -c bcc -at gaff (or amber) This will generate abc.prepin file for your molecule. This will contain the atom name, type and coordinate information. Next step is to derive the parameters for your molecule. ## parmchk -i abc.prepin -f prepi -o abc.frcmod This will give the parameters required to load your molecule in xLeap. Additionally, you should go through the antechamber tutorials at http://ambermd.org/tutorials/basic/tutorial4b/ All the best!!!! Prayagraj Fandilolu Research Scholar, Structural Bioinformatics Unit Department of Biochemistry Shivaji University, Kolhapur - 416004 (MS) India On Thu, Jul 13, 2017 at 5:10 PM, ARMIN HODAEI <ahodaei15.ku.edu.tr> wrote: > Dear AMBER users, > > > Do you know how can I define CMP ligands in xLEAP? I know that > the procedure is to create a prepin file in ANTECHAMBER, but I have no idea > where to start. Has anyone done this before? > > > Sincerely, > -- > Armin Hodaei > Department of Physics, > Faculty of Arts and Sciences > Koc University, Istanbul > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber > ------------------------------ Message: 33 Date: Thu, 13 Jul 2017 12:32:21 +0000 (UTC) From: Saikat Pal <saikatpaliitg.yahoo.com> Subject: Re: [AMBER] Amber installation To: AMBER Mailing List <amber.ambermd.org> Message-ID: <1464176898.5454069.1499949141968.mail.yahoo.com> Content-Type: text/plain; charset=UTF-8 Thank you, Sir, for your kind response. Using Ambertools 17 cpptraj works fine. Can I use xleap of amber 16?? is this work?? Thanks and regards,?Saikat Pal On Thursday 13 July 2017, 5:34:58 PM IST, Daniel Roe <daniel.r.roe.gmail.com> wrote: On Thu, Jul 13, 2017 at 2:18 AM, Saikat Pal <saikatpaliitg.yahoo.com> wrote: > make[2]: Leaving directory '/home/saikat/AMBER/amber-14/amber16/AmberTools/src' > > Installation of AmberTools17 serial is complete at Thu Jul 13 11:19:47 IST 2017. > > make[1]: Leaving directory '/home/saikat/AMBER/amber-14/amber16/AmberTools/src' > ============================================================== > /home/saikat/AMBER/amber-14/amber16//src/Makefile not found, or -noamber was set. > This is expected if you do not have Amber16. > ============================================================== As the message states, AmberTools 17 installed just fine. The last message is just letting you know that you don't have Amber 16, so all is well. > Error: Could not import Amber Python modules! >? ? Probably your Amber Python environment was not set up correctly. > > We recommend adding the line: > >? ? test -f /home/saikat/AMBER/amber-14/amber16//amber.sh? && source /home/saikat/AMBER/amber-14/amber16//amber.sh (sh/bash/zsh) > or >? ? test -f /home/saikat/AMBER/amber-14/amber16//amber.csh && source /home/saikat/AMBER/amber-14/amber16//amber.csh (csh/tcsh) > > to your login shell resource file (e.g., ~/.bashrc or ~/.cshrc). This message is about as clear as error messages get. You need to 'source /home/saikat/AMBER/amber-14/amber16//amber.sh' (or the .csh version if you have C shell). -Dan > Makefile:8: recipe for target 'test' failed > make[1]: *** [test] Error 1 > make[1]: Leaving directory '/home/saikat/AMBER/amber-14/amber16/AmberTools/test' > Makefile:61: recipe for target 'test.serial' failed > make: *** [test.serial] Error 2 > > > > what should I do ??plz help me out. > Thanks and regards, > Saikat Pal > On Wednesday 12 July 2017, 8:51:27 PM IST, Daniel Roe <daniel.r.roe.gmail.com> wrote: > > Use amber16, and source the amber.sh (or amber.csh) file that is > created therein to set up your environment. The only thing from > amber14 that isn't in AmberTools 17 is pmemd, and that does not > require that AMBERHOME is set. > > -Dan > > On Wed, Jul 12, 2017 at 11:01 AM, Saikat Pal <saikatpaliitg.yahoo.com> wrote: >> Dear all, >> I want to install Amber 14 with AMBER 17 tools.When I untar AmberTools17.tar.bz2 it creates amber16 folder and Amber14.tar.bz2 it creates amber14 .There are 2 folders generated.Which one should I export for AMBERHOME?Plz help me out . >> Thanks and regards >> Saikat >> _______________________________________________ >> AMBER mailing list >> AMBER.ambermd.org >> http://lists.ambermd.org/mailman/listinfo/amber > > > > -- > ------------------------- > Daniel R. Roe > Laboratory of Computational Biology > National Institutes of Health, NHLBI > 5635 Fishers Ln, Rm T900 > Rockville MD, 20852 > https://www.lobos.nih.gov/lcb > > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber -- ------------------------- Daniel R. Roe Laboratory of Computational Biology National Institutes of Health, NHLBI 5635 Fishers Ln, Rm T900 Rockville MD, 20852 https://www.lobos.nih.gov/lcb _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amber ------------------------------ Message: 34 Date: Thu, 13 Jul 2017 21:42:16 +0530 From: Martina Devi <martinadevi2011.gmail.com> Subject: [AMBER] cpptraj hbond To: AMBER Mailing List <amber.ambermd.org> Message-ID: <CA+JOZ380P4ngf3oDUaQ8QWUsqu+nkceLZsLiTTWeLUND1X0RJw.mail.gmail.com> Content-Type: text/plain; charset="UTF-8" Dear Amber Users I used the following command to find the H bond between two bases i.e Guanine and Cytosine hbond out hb.dat :1,6 dist 2.5 avgout avg.dat I got the following dat : #Acceptor DonorH Donor Frames Frac AvgDist AvgAng RC3_6.N3 RG5_1.H1 RG5_1.N1 992 0.9920 3.0329 162.1346 RC3_6.O2 RG5_1.H21 RG5_1.N2 976 0.9760 2.9256 162.4696 RG5_1.O6 RC3_6.H41 RC3_6.N4 893 0.8930 2.9950 160.9051 RC3_6.O2 RG5_1.H1 RG5_1.N1 292 0.2920 3.2799 141.3739 RC3_6.N3 RG5_1.H21 RG5_1.N2 25 0.0250 3.3991 139.3231 RC3_6.N4 RG5_1.H1 RG5_1.N1 7 0.0070 3.3845 137.8618 RG5_1.N1 RC3_6.H41 RC3_6.N4 7 0.0070 3.4564 140.1925 RC3_6.O2 RC3_6.HO'2 RC3_6.O2' 2 0.0020 3.2341 139.4926 RC3_6.O3' RC3_6.HO'2 RC3_6.O2' 2 0.0020 2.5560 137.4556 Then I gave the command to find the hydrogen bond of the two adjacent Guanine and cytosine pair hbond out hb.dat :1,6 :2,5 :3:4 dist 2.5 avgout avg.dat But the results showed the same as the above dat file. Where did the script go wrong? Thanks in advance Martina ------------------------------ Message: 35 Date: Thu, 13 Jul 2017 16:21:55 +0000 From: Yao Xiao <yao.xiao26.uga.edu> Subject: [AMBER] ??: About steered MD with pmemd and NMR restraints To: AMBER Mailing List <amber.ambermd.org> Message-ID: <MWHPR02MB2750B3CD41EF3A96AAAA57C791AC0.MWHPR02MB2750.namprd02.prod.outlook.com> Content-Type: text/plain; charset="gb2312" Hi Adrian: Thank you very much for your instruction! I didn't know that. Best Wishes Yao ________________________________ ???: Adrian Roitberg <roitberg.ufl.edu> ????: 2017?7?10? 17:35:58 ???: AMBER Mailing List ??: Re: [AMBER] About steered MD with pmemd and NMR restraints Hi Yao You can use smd in pmemd and in gpu with Amber 16 and a patch, using the ncsu codes. Please look at the amber16 manual for that, sinc ethe input format has changed. adrian On 7/10/17 5:32 PM, Yao Xiao wrote: > Dear Amber Developers: > > > I'm currently trying to run some steered MDs with pmemd. I know many of the sMD features are for sander only, but my systems are too big(~350 protein residues and at least 200ns simulation time) for sander. If I use sander they will take too long to finish. I only know two ways to turn on sMD: ncsu_smd or jar=1. Below is my sample MD input file, which should work for sander: > > > MD production run at NPT > # control section > &cntrl > irest = 1, > ntx = 5, ntb = 2, ntp = 1,ntwprt=4675 > cut = 8.0, ntt = 3, gamma_ln = 2, > ntc = 2, ntf = 2, > tempi = 300.0, temp0 = 300.0, tautp = 2.0, > nstlim = 100000000, dt = 0.002, > ntpr = 30000, ntwx = 10000, ntwv = 0, ntwe = 0, > nmropt = 0, ntr=1, ioutfm =1,iwrap=1,ig = -1, > / > > ncsu_smd > output_file= 'FILE.txt' > output_freq= 10000 > variable > type=MULTI_RMSD > i=(4618, 4636, 4632, 4628, 4621, 4620, 0, 4646, 4664, 4660, 4656, 4649, 4648, 0) > r=(47.228, 38.993, 29.383, > 48.172, 39.346, 30.539, > 47.472, 40.312, 31,486, > 47.010, 41.547, 30.733, > 46.155, 41.145, 29.525, > 46.917, 40.161, 28.700, > > 46.955, 30.894, 40.394, > 47.928, 31.919, 41.011, > 49.322, 31.437, 40.654, > 49.559, 30.004, 41.103, > 48.484, 29.062, 40.595, > 47.239, 29.616, 40.816) > > harm = (10.0) > path = (X,0) path_mode = LINES > end variable > end ncsu_smd > > > In the above MD input file, I'm trying to steer two Glcnac rings (defined as two groups of atoms in "i=" section), towards their position in a known crystal structure(defined as two groups of coordinates in "r=" section.) ,applying a harmonic restraint constant of 10.0. > > This should work for sander, but I just have to use pmend for speed. Since the ncsu_smd codes works for sander only, it appears that I can only do it through jar=1, which requires a restraint file specified by DISANG. It looks to me that whatever the available NMR restraint variable type is, it has to be defined using real atoms present in the system. However, the variable I'm trying to define here involves a group of real atoms and a group of coordinates(no atom is present at these coordinates). > > So to put it together: what NMR restraint variable type can be defined using a group of atoms and a group of coordinates, and also works for pmemd? > > Thank you for providing instructions in advance. > > > > Yao Xiao > Research Assistant > Complex Carbohydrate Research Center > The University of Georgia > Athens, GA, USA > yx55537.uga.edu > > > > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber -- Dr. Adrian E. Roitberg University of Florida Research Foundation Professor Department of Chemistry University of Florida roitberg.ufl.edu 352-392-6972 _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amber ------------------------------ Message: 36 Date: Thu, 13 Jul 2017 13:12:00 -0400 From: Daniel Roe <daniel.r.roe.gmail.com> Subject: Re: [AMBER] cpptraj hbond To: AMBER Mailing List <amber.ambermd.org> Message-ID: <CAAC0qOYb0Ca8p+FwmA0j_oVqOHRZctyFHMHMJfzYVQ3pO5Cezg.mail.gmail.com> Content-Type: text/plain; charset="UTF-8" On Thu, Jul 13, 2017 at 12:12 PM, Martina Devi <martinadevi2011.gmail.com> wrote: > > Then I gave the command to find the hydrogen bond of the two adjacent > Guanine and cytosine pair > hbond out hb.dat :1,6 :2,5 :3:4 dist 2.5 avgout avg.dat This isn't correct usage of the 'hbond' command; you've specified 3 general masks, but cpptraj expects only 1. What you probably want is: hbond out hb.dat :1-6 nointramol dist 2.5 avgout avg.dat Refer to the Amber 17 manual for full syntax details. -Dan > > But the results showed the same as the above dat file. > > Where did the script go wrong? > Thanks in advance > > Martina > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber -- ------------------------- Daniel R. Roe Laboratory of Computational Biology National Institutes of Health, NHLBI 5635 Fishers Ln, Rm T900 Rockville MD, 20852 https://www.lobos.nih.gov/lcb ------------------------------ Message: 37 Date: Thu, 13 Jul 2017 13:18:19 -0400 From: Daniel Roe <daniel.r.roe.gmail.com> Subject: Re: [AMBER] Amber installation To: AMBER Mailing List <amber.ambermd.org> Message-ID: <CAAC0qOY92KP_fVg0og-w2xYsqHfyv7Jt=_xZxZJ8LrGUUu_cLg.mail.gmail.com> Content-Type: text/plain; charset="UTF-8" Just use xleap from AmberTools 17. The environment will already be set up via sourcing that script. -Dan On Thu, Jul 13, 2017 at 8:32 AM, Saikat Pal <saikatpaliitg.yahoo.com> wrote: > Thank you, Sir, for your kind response. Using Ambertools 17 cpptraj works fine. Can I use xleap of amber 16?? is this work?? > Thanks and regards, Saikat Pal > > > > On Thursday 13 July 2017, 5:34:58 PM IST, Daniel Roe <daniel.r.roe.gmail.com> wrote: > > On Thu, Jul 13, 2017 at 2:18 AM, Saikat Pal <saikatpaliitg.yahoo.com> wrote: >> make[2]: Leaving directory '/home/saikat/AMBER/amber-14/amber16/AmberTools/src' >> >> Installation of AmberTools17 serial is complete at Thu Jul 13 11:19:47 IST 2017. >> >> make[1]: Leaving directory '/home/saikat/AMBER/amber-14/amber16/AmberTools/src' >> ============================================================== >> /home/saikat/AMBER/amber-14/amber16//src/Makefile not found, or -noamber was set. >> This is expected if you do not have Amber16. >> ============================================================== > > As the message states, AmberTools 17 installed just fine. The last > message is just letting you know that you don't have Amber 16, so all > is well. > >> Error: Could not import Amber Python modules! >> Probably your Amber Python environment was not set up correctly. >> >> We recommend adding the line: >> >> test -f /home/saikat/AMBER/amber-14/amber16//amber.sh && source /home/saikat/AMBER/amber-14/amber16//amber.sh (sh/bash/zsh) >> or >> test -f /home/saikat/AMBER/amber-14/amber16//amber.csh && source /home/saikat/AMBER/amber-14/amber16//amber.csh (csh/tcsh) >> >> to your login shell resource file (e.g., ~/.bashrc or ~/.cshrc). > > This message is about as clear as error messages get. You need to > 'source /home/saikat/AMBER/amber-14/amber16//amber.sh' (or the .csh > version if you have C shell). > > -Dan > >> Makefile:8: recipe for target 'test' failed >> make[1]: *** [test] Error 1 >> make[1]: Leaving directory '/home/saikat/AMBER/amber-14/amber16/AmberTools/test' >> Makefile:61: recipe for target 'test.serial' failed >> make: *** [test.serial] Error 2 >> >> >> >> what should I do ??plz help me out. >> Thanks and regards, >> Saikat Pal >> On Wednesday 12 July 2017, 8:51:27 PM IST, Daniel Roe <daniel.r.roe.gmail.com> wrote: >> >> Use amber16, and source the amber.sh (or amber.csh) file that is >> created therein to set up your environment. The only thing from >> amber14 that isn't in AmberTools 17 is pmemd, and that does not >> require that AMBERHOME is set. >> >> -Dan >> >> On Wed, Jul 12, 2017 at 11:01 AM, Saikat Pal <saikatpaliitg.yahoo.com> wrote: >>> Dear all, >>> I want to install Amber 14 with AMBER 17 tools.When I untar AmberTools17.tar.bz2 it creates amber16 folder and Amber14.tar.bz2 it creates amber14 .There are 2 folders generated.Which one should I export for AMBERHOME?Plz help me out . >>> Thanks and regards >>> Saikat >>> _______________________________________________ >>> AMBER mailing list >>> AMBER.ambermd.org >>> http://lists.ambermd.org/mailman/listinfo/amber >> >> >> >> -- >> ------------------------- >> Daniel R. Roe >> Laboratory of Computational Biology >> National Institutes of Health, NHLBI >> 5635 Fishers Ln, Rm T900 >> Rockville MD, 20852 >> https://www.lobos.nih.gov/lcb >> >> _______________________________________________ >> AMBER mailing list >> AMBER.ambermd.org >> http://lists.ambermd.org/mailman/listinfo/amber >> _______________________________________________ >> AMBER mailing list >> AMBER.ambermd.org >> http://lists.ambermd.org/mailman/listinfo/amber > > > > -- > ------------------------- > Daniel R. Roe > Laboratory of Computational Biology > National Institutes of Health, NHLBI > 5635 Fishers Ln, Rm T900 > Rockville MD, 20852 > https://www.lobos.nih.gov/lcb > > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber -- ------------------------- Daniel R. Roe Laboratory of Computational Biology National Institutes of Health, NHLBI 5635 Fishers Ln, Rm T900 Rockville MD, 20852 https://www.lobos.nih.gov/lcb ------------------------------ Message: 38 Date: Thu, 13 Jul 2017 13:24:58 -0400 From: Hai Nguyen <nhai.qn.gmail.com> Subject: Re: [AMBER] Amber installation To: AMBER Mailing List <amber.ambermd.org> Message-ID: <CAFNMPM8T3UC=jsu-s+3FE2-7D68sSdvFgTLUJpSZn9m0ounL-Q.mail.gmail.com> Content-Type: text/plain; charset="UTF-8" one more note: The only thing AT17 does not have is pmemd (as Dan said earlier) Hai On Thu, Jul 13, 2017 at 1:18 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote: > Just use xleap from AmberTools 17. The environment will already be set > up via sourcing that script. > > -Dan > > On Thu, Jul 13, 2017 at 8:32 AM, Saikat Pal <saikatpaliitg.yahoo.com> wrote: >> Thank you, Sir, for your kind response. Using Ambertools 17 cpptraj works fine. Can I use xleap of amber 16?? is this work?? >> Thanks and regards, Saikat Pal >> >> >> >> On Thursday 13 July 2017, 5:34:58 PM IST, Daniel Roe <daniel.r.roe.gmail.com> wrote: >> >> On Thu, Jul 13, 2017 at 2:18 AM, Saikat Pal <saikatpaliitg.yahoo.com> wrote: >>> make[2]: Leaving directory '/home/saikat/AMBER/amber-14/amber16/AmberTools/src' >>> >>> Installation of AmberTools17 serial is complete at Thu Jul 13 11:19:47 IST 2017. >>> >>> make[1]: Leaving directory '/home/saikat/AMBER/amber-14/amber16/AmberTools/src' >>> ============================================================== >>> /home/saikat/AMBER/amber-14/amber16//src/Makefile not found, or -noamber was set. >>> This is expected if you do not have Amber16. >>> ============================================================== >> >> As the message states, AmberTools 17 installed just fine. The last >> message is just letting you know that you don't have Amber 16, so all >> is well. >> >>> Error: Could not import Amber Python modules! >>> Probably your Amber Python environment was not set up correctly. >>> >>> We recommend adding the line: >>> >>> test -f /home/saikat/AMBER/amber-14/amber16//amber.sh && source /home/saikat/AMBER/amber-14/amber16//amber.sh (sh/bash/zsh) >>> or >>> test -f /home/saikat/AMBER/amber-14/amber16//amber.csh && source /home/saikat/AMBER/amber-14/amber16//amber.csh (csh/tcsh) >>> >>> to your login shell resource file (e.g., ~/.bashrc or ~/.cshrc). >> >> This message is about as clear as error messages get. You need to >> 'source /home/saikat/AMBER/amber-14/amber16//amber.sh' (or the .csh >> version if you have C shell). >> >> -Dan >> >>> Makefile:8: recipe for target 'test' failed >>> make[1]: *** [test] Error 1 >>> make[1]: Leaving directory '/home/saikat/AMBER/amber-14/amber16/AmberTools/test' >>> Makefile:61: recipe for target 'test.serial' failed >>> make: *** [test.serial] Error 2 >>> >>> >>> >>> what should I do ??plz help me out. >>> Thanks and regards, >>> Saikat Pal >>> On Wednesday 12 July 2017, 8:51:27 PM IST, Daniel Roe <daniel.r.roe.gmail.com> wrote: >>> >>> Use amber16, and source the amber.sh (or amber.csh) file that is >>> created therein to set up your environment. The only thing from >>> amber14 that isn't in AmberTools 17 is pmemd, and that does not >>> require that AMBERHOME is set. >>> >>> -Dan >>> >>> On Wed, Jul 12, 2017 at 11:01 AM, Saikat Pal <saikatpaliitg.yahoo.com> wrote: >>>> Dear all, >>>> I want to install Amber 14 with AMBER 17 tools.When I untar AmberTools17.tar.bz2 it creates amber16 folder and Amber14.tar.bz2 it creates amber14 .There are 2 folders generated.Which one should I export for AMBERHOME?Plz help me out . >>>> Thanks and regards >>>> Saikat >>>> _______________________________________________ >>>> AMBER mailing list >>>> AMBER.ambermd.org >>>> http://lists.ambermd.org/mailman/listinfo/amber >>> >>> >>> >>> -- >>> ------------------------- >>> Daniel R. Roe >>> Laboratory of Computational Biology >>> National Institutes of Health, NHLBI >>> 5635 Fishers Ln, Rm T900 >>> Rockville MD, 20852 >>> https://www.lobos.nih.gov/lcb >>> >>> _______________________________________________ >>> AMBER mailing list >>> AMBER.ambermd.org >>> http://lists.ambermd.org/mailman/listinfo/amber >>> _______________________________________________ >>> AMBER mailing list >>> AMBER.ambermd.org >>> http://lists.ambermd.org/mailman/listinfo/amber >> >> >> >> -- >> ------------------------- >> Daniel R. Roe >> Laboratory of Computational Biology >> National Institutes of Health, NHLBI >> 5635 Fishers Ln, Rm T900 >> Rockville MD, 20852 >> https://www.lobos.nih.gov/lcb >> >> _______________________________________________ >> AMBER mailing list >> AMBER.ambermd.org >> http://lists.ambermd.org/mailman/listinfo/amber >> _______________________________________________ >> AMBER mailing list >> AMBER.ambermd.org >> http://lists.ambermd.org/mailman/listinfo/amber > > > > -- > ------------------------- > Daniel R. Roe > Laboratory of Computational Biology > National Institutes of Health, NHLBI > 5635 Fishers Ln, Rm T900 > Rockville MD, 20852 > https://www.lobos.nih.gov/lcb > > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber ------------------------------ Message: 39 Date: Thu, 13 Jul 2017 11:23:16 -0700 From: Bill Ross <ross.cgl.ucsf.edu> Subject: Re: [AMBER] Amber installation To: amber.ambermd.org Message-ID: <32be4a26-07d1-14c6-6112-9a5468c266cf.cgl.ucsf.edu> Content-Type: text/plain; charset=utf-8; format=flowed Once you have modified .bashrc you need to 'source' it by $ . ~/.bashrc Bill On 7/13/17 4:08 AM, Saikat Pal wrote: > I have added test -f /home/saikat/AMBER/amber-14/amber16//amber.sh && source /home/saikat/AMBER/amber-14/amber16//amber.sh (sh/bash/zsh) in the .bashrc file but same error have shown. What should I do? Actually I want to analyse using AMBERTOOLS 17 for cpptraj.I have AMBERTOOLS 17 And AMBER 14 .please help me out . > Thanks and regards, > Saikat > > > > On Thursday 13 July 2017, 2:05:22 PM IST, Bill Ross <ross.cgl.ucsf.edu> wrote: > > > > On 7/12/17 11:18 PM, Saikat Pal wrote: >> We recommend adding the line: >> >> test -f /home/saikat/AMBER/amber-14/amber16//amber.sh && source /home/saikat/AMBER/amber-14/amber16//amber.sh (sh/bash/zsh) >> or >> test -f /home/saikat/AMBER/amber-14/amber16//amber.csh && source /home/saikat/AMBER/amber-14/amber16//amber.csh (csh/tcsh) >> >> to your login shell resource file (e.g., ~/.bashrc or ~/.cshrc). > > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber > ------------------------------ Message: 40 Date: Thu, 13 Jul 2017 18:38:01 +0000 From: "Li, Wen" <wl2290.cumc.columbia.edu> Subject: [AMBER] ERROR: The unperturbed charge of the unit: is not integral To: "amber.ambermd.org" <amber.ambermd.org> Message-ID: <SN1PR02MB16778FEE03033CDEDE25AAC296AC0.SN1PR02MB1677.namprd02.prod.outlook.com> Content-Type: text/plain; charset="iso-8859-1" Hi Everyone, After a pdb was loaded to leap in order to set up a pmemd run for an RNA+protein system, saveamberparm failed due to the unperturbed charge of the unit is not integral, for example, the charge may be -14.5 or 30.6 etc. Could you please tell me how to get rid of the problem. Thank you! Wen ------------------------------ _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amber End of AMBER Digest, Vol 1994, Issue 1 ************************************** _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Mon Jul 17 2017 - 13:00:02 PDT