[gmx-users] selection around circle
jalemkul at vt.edu
Wed Dec 18 02:11:25 CET 2013
On 12/17/13 7:43 PM, jkrieger at mrc-lmb.cam.ac.uk wrote:
> Thanks Justin,
> I have tried this and I can a new index file that has an item for each frame with atoms that match the selection. How do I create a single index item and combine it into the main index file for use with other tools such as g_hbond?
The output of g_select is not fully compatible with any Gromacs tool, at least
in any pre-5.0 version. Given that I have had not had time yet to fully
investigate the current beta, hopefully someone else can say whether or not the
g_select output is now fully supported by other tools.
> Best wishes
> On 18 Dec 2013, at 00:14, Justin Lemkul <jalemkul at vt.edu> wrote:
>> 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.
>> 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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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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