VMD-L Mailing List

From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Mon Apr 12 2010 - 03:43:25 CDT

Dear all,

I hope this does not count as a cross post (as I have asked a similar
question on the NAMD mailing list as well).

For each frame of my trajectory I would like to calculate all the
side-chain dihedral angles. Similar to the output of this
webservice<http://swift.cmbi.kun.nl/servers/html/chiang.html>.
Currently
I'm planing to export each frame of the trajectory to PDB and using the
excellent Bioshell <http://bioshell.chem.uw.edu.pl/> to calculate dihedral
angles, but probably it would be faster to do this without all the temporary
PDBs (I will have to analyse a lot of short 10 ns trajectories).
A possible way would be to add labels for all the side-chains using "label
add Dihedrals". Could anyone suggest a simpler way?

Thank you,
Ajasja Ljubetič
Young researcher at Jozef Stefan Instiute,
Slovenia, Ljubljana