[gmx-users] pdb2gmx capabilities
Peter I. Hansen
pih at xbase.dk
Fri Jun 10 11:52:25 CEST 2005
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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