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
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Received on Tue Jul 11 2017 - 09:00:02 PDT
