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
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Received on Tue Jul 11 2017 - 14:00:02 PDT
