From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Mon Apr 12 2010 - 02:40:47 CDT
Is there a simple way to calculate all amino acid side-chain dihedral angles
using NAMD? Internally NAMD must already calculate this in order to get the
force-filed energy. Getting just one angle is not a problem using
getdihedral <http://www.ks.uiuc.edu/Research/namd/2.7b2/ug/node44.html>, but
this would be cumbersome for all side-chains.
There is a webservice
dihedral angles, but this is not feasible for a
large trajectory. Currently I'm planing to export each frame of
the trajectory to PDB and using the excellent
but it would be even better if this could be done on the fly.
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 05:22:53 CST