On 6/6/14, 7:22 AM, [email protected] wrote:
hi all, I'm trying to do a simulation of a membrane protein in DPPC, with Gromacs4.6. I used gromos96 53a6 as forcefield. I'm following KALP15 tutorial of gromacs. I'm trying to orient protein in membrane but I can't with editconf because I don't know what parameters I had to use as center of mass. I've tried to move the membrane in the correct orientation with vmd but when I do the energy minimization, the membrane change position. how to fix it?
editconf is the proper tool to use to place the protein. Leave the membrane alone; manipulate the protein's coordinates. editconf provides all the options you need to align, translate, or rotate the protein. Identifying the proper orientation can be challenging, but based on the composition of the transmembrane domain and its dimensions, it should be easy to construct a rough guess that should equilibrate and reorient as needed over time.
-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 [email protected] | (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 [email protected].
