[gmx-users] Error in system_inflate.gro coordinates does not match
jalemkul at vt.edu
Wed Jul 23 19:20:39 CEST 2014
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
> 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 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
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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