calculate side-chain dihedral/torsion angles

From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Mon Apr 12 2010 - 02:40:47 CDT

Dear all,

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
<http://swift.cmbi.kun.nl/servers/html/chiang.html>to calculate
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
Bioshell<http://bioshell.chem.uw.edu.pl/>,
but it would be even better if this could be done on the fly.

Best regards,
Ajasja

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