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
Received on Wed Jul 12 2017 - 08:00:03 PDT
