[gmx-users] How to create a gmx topology for a polysaccharide using glycam 06?

Davide Mercadante dmer018 at aucklanduni.ac.nz
Tue May 1 08:18:32 CEST 2012

Dear gmx users,

please accept my apologies if mine is a stupid question or it has already
been done to you. I have been looking at the mailing list but I was unable
to find any satsfying answer to my problem. I am going to run MD on a
homogalacturonan chain (polysaccharide like chain composed by
a-D-galacturonic acid residues) with different degree of methylation.

The parameters for the monomers composing the HG chains have already been
parametrized and are included in the glycam 06 forcefield. I want to use
this forcefield (glycam) to run my simulations.

Is there an automated way to create a gromacs topology using a pdb file?
Can PRODRG, ATB, or any other programs create the gromacs topology
(including glycam parameters) for my molecule?

Any help will be very much appreciated.

Thank you in advance for your time.

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