[gmx-users] pdb2gmx capabilities

David van der Spoel spoel at xray.bmc.uu.se
Fri Jun 10 14:53:10 CEST 2005

On Fri, 2005-06-10 at 11:52 +0200, Peter I. Hansen wrote:
> 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 
> conformation.
> 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?
you can use pdb2gmx for any polymer as long as you use the right
building blocks (rtp and hdb files) and options (-ter to turn off
protein-centric termini generation).

How useful the existing GLC* blocks are I don't know, they were used in
the early 90ties in the Berendsen group.
> I thank you in advance.
> Peter
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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