[gmx-users] Charmm to gromacs conversion for lipids

Venkat Reddy venkat4bt at gmail.com
Wed Nov 5 13:33:19 CET 2014

Dear Justin,
My lipid is cholesteryl oleate (CO). Since there are CHARMM36 parameters
available for cholesterol and oleate chain in POPC, I have clubbed both
together to generate the topology for CO (rtf file). Now I want to convert
this rtf to itp file. is there any shortcut to accomplish this task?

On Wed, Nov 5, 2014 at 5:57 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

> 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
> --
> ==================================================
> 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
> http://mackerell.umaryland.edu/~jalemkul
> ==================================================
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With Best Wishes
Venkat Reddy Chirasani
PhD student
Laboratory of Computational Biophysics
Department of Biotechnology
IIT Madras

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