[gmx-users] gmx select

Justin Lemkul jalemkul at vt.edu
Thu Jul 13 16:18:08 CEST 2017

On 7/13/17 10:01 AM, Pandya, Akash wrote:
> So I tried with both opening and closing. It seems to select all the molecules in my box which is not what I want. I only want certain glycine molecules that are closest to the protein. May you please suggest another way is which I could achieve this. The command I used is below:
> gmx select -f output.xtc -s output.gro -select '"Close to protein" resname Glycine and within 0.5 of group "Protein"' -pdbatoms selected -ofpdb

"resname Glycine" surely will return nothing.  You need to use valid residue 
names as found in the .gro file.  The format of .gro permits residue names up to 
5 characters, so clearly "Glycine" is never going to match anything.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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