autoimage is cpptraj-only.
On Wed, Dec 5, 2012 at 8:53 AM, Hirdesh Kumar <hirdesh.iitd.gmail.com>wrote:
> 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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> >
>
>
>
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed Dec 05 2012 - 07:00:03 PST
