[gmx-users] getting internal coordinates for artificial peptide

[Chris Gaughan]

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?

Thanks
Chris G  

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