[gmx-users] empty index group

Justin Lemkul jalemkul at vt.edu
Thu Apr 21 13:33:32 CEST 2016

On 4/21/16 7:29 AM, David Newman wrote:
> Hi,
> So on Gromacs 4.6.5, I'm using the make_ndx command to try to create a custom
> index of a binding pocket on my protein of interest, I want to group 5
> non-contiguous residues, I can index them separately and tried to group them
> with & but that creates an empty group error because I guess it is for
> linking separate options together not separate instances of the same option.
> Is there a way to achieve what I'm after?

Your problem is that you used &.  Atoms cannot be in one residue and 
simultaneously in another.  You need the "or" operator, |, e.g.:

r 10 | r 20 | r 30 | r 40 | r 50

because atoms can be in residue 10 OR residue 20 OR ...



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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