[gmx-users] getting internal coordinates for artificial peptide
spoel at xray.bmc.uu.se
Wed Apr 27 22:21:38 CEST 2005
On Wed, 2005-04-27 at 13:10 -0700, Chris Gaughan wrote:
> I am trying to generate coordinates for two small
> peptides. There is no pdb reference for these peptides
> because they are artificial. In my efforts to generate
> .gro file for these peptides, I tried the dundee
> prodrg2 server. This server allows you to draw small
> molecules in a JME editor and it will use the drawing
> to generate .gro and topology files. Unfortunately, my
> peptide was too big and could not be processed.
> Does anyone know another wayI could generate topology
> files for these peptides?
Use pymol to build a pdb.
> Chris G
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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