On 6/14/16 1:53 PM, Mohsen Ramezanpour wrote:
Dear Gromacs users, I am trying to parameterize a lipid molecule with a weird headgroup :-) in Charmm36 force field for doing simulation in GROMACS. Reading through literature, I found that Swissparam, and Paramchem.org are two useful tools to make the topology files automatically. However, both seems to be suitable for small drug-like molecules than large biological molecules, like lipids. Swissparam is a mixture of charmm parameters and MMFF and is not based on any specific CHARMM FF version. Paramcharm has also recommended to not use it for biological molecules. Although lipids are biological molecules, but I was wondering what will happen if we consider the "whole synthetic lipid" as a drug-like molecule. In this case, we might be able to mix it with other lipids which have been parameterized in Charmm36?
You should start by using any relevant parameters from the CHARMM36 lipid force field, then parametrizing new moieties to be consistent with the lipid force field using suitable model compounds. CGenFF might give OK estimates of initial charges, dihedrals, etc. but they should absolutely not be directly combined or considered final. They'll point you in the right direction, but hybridizing CGenFF and highly optimized protein/nucleic acid/lipid force fields within the same molecule is not a proper approach.
-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.
