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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Received on Tue Dec 04 2012 - 08:00:02 PST
