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

[Justin Lemkul]

On 4/14/14, 4:33 PM, sbowerma wrote:
> Hello all,
>
> I am currently looking at the g_chi analysis tool.  I would like to create a
> time distribution of dihedral angle values for a dna-protein system, with
> the end-goal of using this distribution in a mutual information calculation.
> Unfortunately, I see that the g_chi tool is limited to only amino acid
> residue dihedrals, and the dna-protein interactions are vital to my
> interests.  I have done a search for a work around to this issue that has
> (so far) been unfruitful.  Now I am coming to the GROMACS community to see
> if anyone can point me to a tool of this kind to save me the headache of
> trying to alter the current one.  I am already aware that ptraj in AMBER can
> do a similar task (which is my current venue of attack), but it requires
> (either by script or user "hand-entry") a list of all dihedrals of interest
> (I will be doing this analysis on many more than one trajectory and one
> system configuration!).  Thanks in advance!
>

Time series for any dihedrals can be obtained with g_angle -type dihedral.  See 
g_angle -h for more helpful options.

-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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