From: Axel Kohlmeyer (
Date: Mon Apr 12 2010 - 05:43:37 CDT

On Mon, Apr 12, 2010 at 4:43 AM, Ajasja Ljubetič
<> wrote:
> 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. Currently I'm planing to export each frame of
> the trajectory to PDB and using the excellent Bioshell 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?

not sure about simpler, but definitely more efficient would be
to use tcl scripting in VMD.

you can get the list of dihedrals from the topotools plugin
(or even use the generate those, in case you don't have
a suitable topology file with existing definitions. topotools
commands accept a -sel option that you can give a selection
string or a selection command as argument, which would
restrict the list to dihedrals fully contained in the sidechain.

then you can loop over those and either use the measure
or label command to compute the dihedral angle values
for your trajectory. probably label would be more efficient.


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

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.