[gmx-users] coordinates, topology and PRODRG

Lars Poulsen lpoulsen at chem.au.dk
Thu Nov 22 18:04:18 CET 2001

Dear Eric, Daan and David,

Thank you for the answers!
I have previously tried to use x2top as David suggested, but I've never gotten past the core dumps.

I was initially a bit hesitant to try pdb2gmx, because I didn't quite understand the 'bio terminology'. But combining your answer to the following strategy seems to work:
1) PRODRG to create the monomer topologies for the .rtp file
2) and then pdb2gmx for the .gro and .top files.
I don't seem to have to worry about the .hdb file, since I want to use UA. 
I don't quite understand the .tdb file, but manually changing the atom type for the first and last atom in the chain is no problem.

This means, I can now use the slow MSI software for generating amorphous polymer cells as input for GROMACS and no longer have to rely on MD-simulations to contract a 'manually' made stretched polymer chain. 

Thanks, best regards, Lars
Lars Poulsen
Dept. of Chemistry, University of Aarhus
Langelandsgade 140, DK-8000 Aarhus C
Phone: +45 8942 3871
Fax: +45 8619 6199
email: lpoulsen at chem.au.dk

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