[gmx-users] selection around circle
jalemkul at vt.edu
Wed Dec 18 01:15:58 CET 2013
On 12/17/13 1:55 PM, jkrieger at mrc-lmb.cam.ac.uk wrote:
> I think g_select does something like this. I am trying to do something
> similar: make a selection of water within 5A or so of a residue in my
> protein. Also need help please.
The examples at the end of g_select -select 'help all' pretty well cover most of
these situations. What have you tried? What has it given you? Something like:
same residue as resname SOL and within 0.5 of residue X
provided that residue X is defined within an .ndx file provided on the command,
line should work. Disclaimer: this is just off the cuff, but probably pretty close.
>> Dear Gmx Users,
>> I have my carbon nanotube (lenght z axis) with proteins attached to it. I
>> wish to collect RDF of given type of amino acids away from the surface in
>> two dimensions (xy). Z axis does not interest me. That would make a circle
>> then. My question: how to make a specific index group of this circle? Any
>> ideas appreciated.
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Justin A. Lemkul, Ph.D.
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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