[gmx-users] Select atoms in a residue

Justin Lemkul jalemkul at vt.edu
Tue Sep 3 15:02:34 CEST 2013

On 9/3/13 8:57 AM, ABEL Stephane 175950 wrote:
> Hello all,
> A Quick question below:
> My peptide contains one trp, and i want to select only the atoms that form the the indol ring. I would like a portable script for others systems that contain also a peptide with one Trp residue. So I am not interesting to select the corresponding atoms by their numbers in the pdb/gro files
> The atom name in the indol group are  aCG | aCD1 | aHD1 | aCD2 | aCE3 | aHE3 | aCZ3 | aHZ3 | aCH2 | aHH2 | aCZ2 | aHZ2 | aCE2 | aNE1 | aHE1
> Can you help me ?

What is the problem?  Aside from a lack of a space between the 'a' and the 
actual atom name, that should work just fine.



Justin A. Lemkul, Ph.D.
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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