[gmx-users] pdb2gmx capabilities

Peter I. Hansen pih at xbase.dk
Fri Jun 10 11:52:25 CEST 2005

Hello users

I'm looking into using gromacs for my work, but having some 
problems since pdb2gmx only seems to expect peptides.

I have been trying to modify the gmxdemo/demo script to run 
molecular dynamics on glucose. Since the GLCA unit is not 
complete I've tried to hack it together by adding an H and OH 
from water, without much luck.

I've looked at the prodrg website, which is nice, but not so 
usefull if you want to build a oligosaccharide with a certain 

So, my questions are these. Is pdb2gmx only intended for peptide 
work? Do any of you know of a way to build gromacs topologies 
from pdb/mol2/xyz format files?

I thank you in advance.


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