[gmx-users] getting internal coordinates for artificial peptide

[David]

On Wed, 2005-04-27 at 13:10 -0700, Chris Gaughan wrote:
> Hello,
> 
> 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.
> 
> Thanks
> Chris G  
> 
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-- 
David.
________________________________________________________________________
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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