On 8/12/14, 11:08 AM, Wainwright, Josh wrote:
Thanks for the prompt response Justin. We are working with protein fragments with between 1 and 3 helices. I've noticed that Anirban Ghosh made a tutorial based on yours, and he used Gromos43a1 for a GPCR (7 helices) in bacterial membranes (POPC in his case, as opposed to DPPC in your case with the model KALP-15 protein). Do you think 43a1 is a good alternative, or is there any other forcefield you would recommend?
43A1 or 54A7 would probably be better.
I've also seen people recommend CHARMM36.
CHARMM36 has excellent lipid parameters, better than Berger for most observables. -Justin -- ================================================== Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 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.
