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
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
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 Tue Dec 04 2012 - 09:30:02 PST
