Hello,
thank you very much for your suggestions, but neither the Thomas nor the
InSuk ones work...
I suspect that Thomas is right and the imaging is pathologic... which also
relates with wrapping. May be I need to do some programming for my own, if
nobody else have an idea.
Thank you very much and regards
A.
On Tue, May 10, 2011 at 6:49 PM, InSuk Joung <i.joung.gmail.com> wrote:
> Hi,
> Try the following two step processing:
>
> #### first ptraj run ####
> trajin tic_md_1.mdcrd 1 10000
> unwrap :1-436
> image center :* familiar com :1-436
> trajout temp.mdcrd
>
> #### second ptraj run ####
> reference tic.rst7
> trajin temp.mdcrd 1 10000 200
> rms reference out tic_md_rmsd_new.dat .CA,C,N
>
>
> On Tue, May 10, 2011 at 12:09 PM, Alex Rodriguez <alexdepremia.gmail.com
> >wrote:
>
> > Hello everybody,
> >
> > I'm having what seems to be a system imaging problem, and I'm not able to
> > solve it.
> >
> > I'm performing a pretty long trajectory (70 ns) on a protein dimer with
> two
> > non-protein substrates (4 solute molecules). I performed it with PME in a
> > cubic box and with iwrap=1.
> >
> > The question, is that when performing the rmsd analysis, it leads to
> > unrealistic results. As recommended in the list, I tried to center the
> > image. The ptraj script that I employed is:
> >
> > reference tic.rst7
> > trajin tic_md_1.mdcrd 1 10000 200
> > center :1-217 mass origin
> > image origin center
> > center :1-434 mass origin
> > image origin center
> > center :1-435 mass
> > image origin center
> > center :1-436 mass
> > image origin center
> > rms reference out tic_md_rmsd_new.dat .CA,C,N
> >
> > And the output is attached.
> >
> > Any suggestion?
> >
> > Thanks in advance
> >
> > Alex
> >
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
>
>
> --
> Best,
> InSuk Joung
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> AMBER.ambermd.org
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>
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Received on Tue May 10 2011 - 11:00:02 PDT
