On 7/23/14, 12:12 PM, RINU KHATTRI wrote:
hello everyone thank you justin but how can i increase the box size i am using the box vector which is present in popc_whole.gro how can i edit it
editconf
and one more problem when i see it in vmd my ligand is out side the protein
Position the protein-ligand complex like you want before packing the lipids around the protein, remove the ligand, then assemble the membrane protein system. With strong restraints, the protein should not move, so you can just paste in the ligand coordinates afterwards. Then adjust the box and solvate.
-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.
