[gmx-users] Charmm to gromacs conversion for lipids
jalemkul at vt.edu
Wed Nov 5 13:35:47 CET 2014
On 11/5/14 7:33 AM, Venkat Reddy wrote:
> 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?
In theory, our conversion script should handle that, because all the .str files
are are .rtf and .prm entries, so if you don't have any new parameters, it can
probably convert the .rtf itself. Never tried it, but you can probably make it
work. Error messages are pretty descriptive in case of any issues.
> 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
>>> 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
>>> 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
>> 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
>> Gromacs Users mailing list
>> * Please search the archive at http://www.gromacs.org/
>> Support/Mailing_Lists/GMX-Users_List before posting!
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
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
More information about the gromacs.org_gmx-users