Hi Bill,
Could you explain a little bit more about "image minimizer"...my
understanding is to write a small script that try all different orders of
center-image...?
Best,
Guqin
On Sat, Jul 8, 2017 at 10:22 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> What's needed is an image minimizer that tries all neighboring box
> placements for all molecules.
>
> Bill
>
>
> On 7/8/17 7:06 PM, Guqin Shi wrote:
> > 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
> >>
> >
> >
>
>
> _______________________________________________
> 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 - 21:00:02 PDT
