[gmx-users] coordinates, topology and PRODRG

[Daan van Aalten]

Hi Lars

The word poly-mer suggests there is/are monomer(s) to be found in there
somewhere. Why not build a monomer topology, put it in the GMX residue
library and then link it together?

cheers

Daan


On Wed, 21 Nov 2001, Lars Poulsen wrote:

> Dear all,
> 
> Are there any other tools out there for converting pdb coordinates to gromacs coordinates and creating topologies than the PRODRG server?
> 
> The PRODRG server is great, but since I would like to convert and create topologies for large polymer systems, I can't really limit myself to the 100 atoms allowed.
> 
> Any suggestions?
> 
> Best regards,
> Lars Poulsen
> -----------------------------------------------------------------
> 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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##############################################################################
 
Dr. Daan van Aalten                    Wellcome Trust RCD Fellow 
Wellcome Trust Biocentre, Dow Street   TEL: ++ 44 1382 344979 
Div. of Biol.Chem. & Mol.Microbiology  FAX: ++ 44 1382 345764 
School of Life Sciences                E-mail: dava at davapc1.bioch.dundee.ac.uk
Univ. of Dundee, Dundee DD1 5EH, UK    WWW: http://davapc1.bioch.dundee.ac.uk 

        O     C           O     C         Visit the PRODRG server to take 
        "     |           "     |         the stress out of your topologies!
  N--c--C--N--C--C--N--C--C--N--C--C--O   
     |           "     |           "      http://davapc1.bioch.dundee.ac.uk/
     C-C-O       O   C-C-C         O             programs/prodrg/prodrg.html
       "         
       O