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
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Received on Tue Jul 11 2017 - 13:00:02 PDT
