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
Received on Wed Jul 12 2017 - 07:30:03 PDT
