Or maybe I can replace these two files under my current
$AMBERHOME/AmberTools/src/cpptraj/src directory..?
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
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Received on Wed Jul 12 2017 - 07:00:06 PDT
