Just for curiosity i wanted to know whether this works with ptraj as well ?
(I mean above mentioned commands work only with cpptraj or also with ptraj?
On Tue, Dec 4, 2012 at 6:00 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> You need to use a topology that corresponds to your stripped
> coordinates. You can easily generate one with cpptraj - I also
> recommend using autoimage in cpptraj. The cpptraj script would be:
>
> trajin protein_prod.mdcrd 1 150 1
> strip :WAT outprefix strip
> autoimage
> rms first out rmsd.out .CA,C,N
> trajout protein_prod_centered.mdcrd nobox
>
> Assuming your input topology is named something like "protein.prmtop",
> the strip command will generate a stripped topology named
> "strip.protein.prmtop", which you can then using along with your
> stripped trajectory "protein_prod_centered.mdcrd".
>
> You can also use the parmed program to create a stripped topology.
>
> Hope this helps,
>
> -Dan
>
> On Tue, Dec 4, 2012 at 8:56 AM, Fabian Glaser <fglaser.technion.ac.il>
> wrote:
> > Hi all,
> >
> > I am trying to center all trajectory frames after simulation, as
> suggested in several tutorials and manual:
> >
> > trajin protein_prod.mdcrd 1 150 1
> > trajout protein_prod_centered.mdcrd nobox
> >
> > rms first out rmsd.out .CA,C,N
> >
> > center :1-122 mass origin
> > image origin center familiar
> >
> > strip :WAT
> >
> > The rmsd looks fine, but when I run the MD movie application in Chimera
> with the re-centered coordinates file, the result looks horrible, the bonds
> of the protein are wrong and not all the frames are uploaded.
> >
> > What am I doing wrong?
> >
> > Thanks a lot in advance,
> >
> > Fabian
> >
> >
> >
> > _______________________________
> > Fabian Glaser, PhD
> > Bioinformatics Knowledge Unit,
> > The Lorry I. Lokey Interdisciplinary
> > Center for Life Sciences and Engineering
> >
> > Technion - Israel Institute of Technology
> > Haifa 32000, ISRAEL
> > fglaser.technion.ac.il
> > Tel: +972 4 8293701
> > Fax: +972 4 8225153
> >
> >
> > _______________________________________________
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>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 201
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-9119 (Fax)
>
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Received on Wed Dec 05 2012 - 06:00:04 PST
