Hi Dan,
Thanks for reply.
Yes, the first I've thought of is to use "autoimage" directly. I have to
admit it worked unexpectedly well. But for the late ns trajectories, it
failed, too. It has the same result as the one I got from the separate
center-and-image...
Best,
Guqin
On Sat, Jul 8, 2017 at 8:02 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> Try the 'autoimage' command in cpptraj and see if that works for you.
>
> -Dan
>
> On Sat, Jul 8, 2017 at 6:59 PM Guqin Shi <shi.293.osu.edu> wrote:
>
> > Dear all,
> >
> > My simulation is on a huge complex containing 6 molecules. To visualize
> the
> > trajectory and get "correct" coordinates, I usually center-n-image the
> > coordinates... I used to center on 1 molecule, image, and then center on
> 2
> > molecules (include the first one), and then image; and eventually center
> on
> > 6 molecules and image, as suggested in some amber mailing list posts. It
> > worked well.
> >
> > ex.
> > center :1-300 origin (molecule 1)
> > image center origin
> > center :1-500 origin (molecule 2)
> > image center origin
> > center :1-650 origin (molecule 3)
> > image center origin
> > center :1-950 origin (molecule 3)
> > image center origin
> > center :1-1150 origin (molecule 4)
> > image center origin
> > center :1-1300 origin (molecule 6)
> > image center origin
> >
> > However, as the molecules deviates during the simulation, after applying
> > the above commands, there is always one molecule (it could be different
> > molecule dependent on the order I center-image on different masks...)
> that
> > just couldn't be placed back... no matter how different combinations I
> have
> > tried...
> >
> > My first question is that does it make sense that the above commands work
> > well for first quite a few ns of trajectories but failed to wrap for the
> > late ns of trajectories...?
> >
> > The second one will be if there is any tips or suggestions or starting
> > point that I could try out? I have tried different combinations, starting
> > center on different molecule(s), I just couldn't get all 6 back to the
> > correct place...
> >
> > I also tried to center on reference structure...but it just put molecule
> > onto the geometric center, the direction is still off...I don't know how
> to
> > center molecules onto a suitable place so that all 6 could be fit into
> one
> > box...That doesn't make sense...I mean I start with an intact complex...
> >
> >
> > Thank you for any thoughts!
> > Best,
> > Guqin
> >
> >
> >
> > --
> > 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 Sat Jul 08 2017 - 19:30:02 PDT
