[gmx-users] dihedral angle g_angle?

[Justin Lemkul]

On 11/21/14 5:12 AM, Urszula Uciechowska wrote:
> HI
> I use   mk_angndx   to     produce      angle.ndx
> then, I entered  g_angle -od angdist.xvg -ov angaver.xvg -type dihedral
>
> it follows the options:
>
> Group     0 ( Phi=0.0_3_0.60) has   368 elements
> Group     1 ( Phi=0.0_2_4.92) has   368 elements
> Group     2 ( Phi=0.0_3_0.65) has  1104 elements
> Group     3 ( Phi=0.0_3_1.60) has   736 elements
> Group     4 (Phi=180.0_2_0.42) has   552 elements
> Group     5 ( Phi=0.0_3_1.60) has   528 elements
> Group     6 ( Phi=0.0_3_0.75) has   368 elements
> Group     7 (Phi=180.0_2_1.05) has   368 elements
> Group     8 (Phi=180.0_1_0.84) has   368 elements
> Group     9 ( Phi=0.0_2_2.72) has   184 elements
> Group    10 (Phi=0.0_1_10.46) has   184 elements
> Group    11 ( Phi=0.0_0_0.00) has   552 elements
> Group    12 (Phi=180.0_2_7.11) has   184 elements
> Group    13 (Phi=180.0_2_6.90) has   368 elements
> Group    14 (Phi=180.0_2_41.84) has    92 elements
> Group    15 (Phi=180.0_2_10.67) has   288 elements
> Group    16 (Phi=180.0_2_12.55) has   208 elements
> Group    17 (Phi=180.0_2_22.80) has   368 elements
> and it goes up to group 82.
> My system is a protein and would like to analyse the dihedral angles. Is
> it possible for a protein systems? or this is only for the peptides?
> which group should I pick up?
>

mk_angndx makes index files based on dihedral types, e.g. those with the same 
parameters.  You'd have to reference the topology and ffbonded.itp to see which 
groups correspond to what, or create index groups of interest manually or via 
make_ndx.

-Justin

-- 
==================================================

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
http://mackerell.umaryland.edu/~jalemkul

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