[gmx-users] Error in system_inflate.gro coordinates does not match

Justin Lemkul 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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