[gmx-users] pdb2gmx capabilities

David van der Spoel spoel at xray.bmc.uu.se
Fri Jun 10 16:31:38 CEST 2005

On Fri, 2005-06-10 at 15:39 +0200, Peter I. Hansen wrote:
> > 
> > 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.
> The GLC* blocks are strangely incomplete. I tried to build a 
> GLCA unit topology with PRODRG, and this gave me completely 
> different charges.
> In a paper from 1996 (journal of computational chemistry, vol. 
> 17, no. 8, pp. 1068--1084) Ott and Meyer parametrize the gromos 
> forecefield for oligosaccharides, but I guess these parameters 
> never made it into the program. The data from the paper are not 
> accesible.
> Do you recommend I try to build a new GLCA unit from PRODRG, or 
> try to expand the existing one?
You can start with prodrg and use the topology as a template for
building blocks. It will involve manual labor, but if you are going to
do a lot of these then it is the best option. You may also want to
consider the OPLS force field.

> /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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