[gmx-users] getting internal coordinates for artificial peptide

[Cesar Lopez]

Well I suposse that it is only necessary to build de peptide with the software that you want, for example pymol or Hyperchem, wathever. Save the construct in pdb format with the amino and carboxil end correctly.
Cesar

David <spoel at xray.bmc.uu.se> wrote:
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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