[gmx-users] Charmm to gromacs conversion for lipids

Justin Lemkul jalemkul at vt.edu
Wed Nov 5 13:27:24 CET 2014

On 11/5/14 7:03 AM, Venkat Reddy wrote:
> Thank you Joao for the quick reply. My system has single lipid molecule and
> I have pre- calculated charge information for every atom in the lipid. I
> have edited charges on individual atoms apart from atom types.
> By the way, Previous studies have reported a topology for same lipid but in
> NAMD convention. Is there any other tool to convert NAMD to GROMACS
> compatible format?

You have to be careful here.  I would not use CGenFF for lipids, but for reasons 
different than what Joao was saying.  As is cautioned in the CGenFF description, 
you shouldn't use it for molecules for which a highly tuned biomolecular force 
field already covers much of, if not all, of the chemical space.  The CHARMM36 
lipid force field is highly optimized and performs very well.  CGenFF, by its 
nature, is generalized.  With generalization and increased transferability comes 
a decrease in accuracy.  Coupling charges calculated by a different method (is 
it compatible with what CHARMM normally requires, and are those charges tuned 
against the LJ parameters of the atom types to give reasonable intermolecular 
and water-water interactions?) with somewhat less accurate atom types and bonded 
parameters will probably lead to a poor result because you've got a hodge-podge 
of a topology.

What is this lipid that you're trying to parametrize?  Are its functional groups 
covered by the existing parameters in the CHARMM36 lipid force field?  If they 
are, you should absolutely be using those parameters (charges, atom types, and 
bonded parameters).  Even small inaccuracies or imbalances can have a huge 
impact, especially on lipids, which are very sensitive.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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