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
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Received on Sat Jul 08 2017 - 17:30:02 PDT
