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 <jalem...@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 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > ================================================== > -- > 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-requ...@gromacs.org. > -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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-requ...@gromacs.org.