[gmx-users] mk_angndx

Andrei Neamtu neamtuandrei at gmail.com
Sun Jul 4 14:48:15 CEST 2010

Hi all,

I am trying to make a PCA analysis of an protein md trajectory in
dihedral space. Anyway I don't really understand how to use mk_angndx
. When I run this command:

mk_angndx -s ../foo.tpr -n dangle.ndx -type ryckaert-bellemans

it seems that the resulting index file contains all the dihedrals in
the tpr structure file grouped by the force constant of the first
Ryckaert-Bellemans coefficient, but I want only the phi-psi dihedrals.

Is there a way of doing this?


 Dr. Andrei Neamtu, PhD, Lecturer
 Dept. of Physiology
"Gr. T. Popa" Iasi University of Medicine and Pharmacy
 str. Universitatii nr. 16
 IASI, Jud. Iasi

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