VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Thu Sep 11 2008 - 08:52:36 CDT

You should be able to do this with the measure dihed command (see
http://www.ks.uiuc.edu/Research/vmd/current/ug/node124.html), which
returns a list with the value of the selected dihedral at each timestep.
You'd just need to wrap it in an appropriate loop to go over all
residues you want, and each torsion within each residue that you care about.
Best,
Peter

mon_sharma_at_research.iiit.ac.in wrote:
> Dear All,
> I am working on simulations of RNA molecules, using NAMD. I wish to
> calculate the various torsion angles values for each nucleotide at
> timestep frame.
> I have used X3DNA also on PDB files, but I am getting values only for
> the paired base pairs, and moreover, data also does not seem to be
> easily 'parsable'. I want to calculate the values for all the 6 of
> these angles.
> If anyone can help me out or if its somehow possible through VMD. All
> suggestions are
> welcome. Thanks,
> Regards,
> Monika Sharma
>