[gmx-users]build topology file for a molecule define with new residues

Justin A. Lemkul jalemkul at vt.edu
Thu Feb 21 17:34:00 CET 2008

Quoting cilpa at users.csc.fi:

> hi all,
> i would like make MD simulation of heparin. the only files i have is the
> pdb file from protein data bank but residues in this file are unknown by
> gromacs. so i have to build the topology file. Is anyone had ever built
> topology files and parameters files [or have any ideas] and could help in
> telling me the main steps to create those files?

Parameterization questions are asked almost daily.  Check the archive for such
inquiries about drugs, ligands, etc.  (I just replied to one this morning, as a
matter of fact).  Standard reading for such problems:



The PRODRG server can be used to generate primitive GROMOS topologies, but be
advised that the charges given in these topologies are often unsatisfactory.


> geraldine cilpa
> Helsinki university
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080


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