[gmx-users] g_chi-like analysis for nucleic acid residues

[Justin Lemkul]

On 4/14/14, 5:09 PM, sbowerma wrote:
> Hi Justin,
>
> Thanks for your response.  I did see the g_angle tool, but doesn't it have a
> similar limitation as AMBER's ptraj?  From what I can see, I would still
> need to script out an index file for every single dihedral atom set of
> interest (which is all of them and I have over 1k residues).  While this is
> of course do-able, I was looking for more of an "intelligent" tool, like
> g_chi, that already knows dihedral definitions after you pass it a pdb full
> of residue names (or something equivalent).  As I mentioned, I will be doing
> this analysis for several different systems, so I am just trying to figure
> out what tools are worth my time developing and what tools are already being
> used.  Thanks again!
>

You can do all the analysis at once if you design suitable index groups with 
mk_angndx or make_ndx.  Dump out all the time series simultaneously with g_angle 
-all, then post-process to your heart's content.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA 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
http://mackerell.umaryland.edu/~jalemkul

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