[gmx-users] dihedral angle g_angle?
jalemkul at vt.edu
Fri Nov 21 13:33:13 CET 2014
On 11/21/14 5:12 AM, Urszula Uciechowska wrote:
> 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
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
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