Hey Dan,
I know, right... The system is just a little bit special... Thanks for your
suggestion. I will try it right away! But before that I still have some
technical questions..
I am wondering if the file format matter a lot here?
For example, for the original input coordinates: I usually save a copy of
pdb file after tleap is done (when preparing prmtop and inpcrd). And that
pdb file is definitely the "correct" form. Or is .rst the best file as
reference since an "unwrap" will be performed later? Also, I think I only
have .rst instead of .rst7...I hope this isn't a big issue...?
Again, you trajin netcdf format of coordinates while I only have .crd
files, I hope these two won't be a problem either...
Last is I am a little bit confused by this sentence "make certain you
unwrap the trajectory in the right order, i.e. in the same order it was
simulated."...I am not sure how I can achieve that...I can find a .rst file
with "correctly" formed shape, if that is what "the right order" means...?
Thanks a lot! I will test it and let you know if it works!
-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 <http://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 - 07:00:02 PDT
