VMD-L Mailing List

From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Mon Apr 12 2010 - 06:38:16 CDT

Yes, I have tried that, actually. But I get too many dihedrals (not just the
IUPAC Chi1, Chi2 .. Chi4 but all possible dihedral angle combinations). I
have not yet figured out how to filter them.
What is the first value in the list of dihedral angles? The 'topo
getdihedrallist -sel "protein and resid 18"' returns a list of
lists {unknown 215 217 223 224} {unknown 215 217 219 220} .... Does
"unknown" refer to the dihedral name? Or is the type meant to be improper or
dihedral angle?

I'm using the 1.1 version of topotools. And I have loaded the molecule from
a psf/pdb combination.

Best regards,
Ajasja Ljubeti

On Mon, Apr 12, 2010 at 12:43, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> On Mon, Apr 12, 2010 at 4:43 AM, Ajasja Ljubeti
> <ajasja.ljubetic_at_gmail.com> 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.
>
> cheers,
> axel.
>
> > Thank you,
> > Ajasja Ljubeti
> > Young researcher at Jozef Stefan Instiute,
> > Slovenia, Ljubljana
>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com
> http://sites.google.com/site/akohlmey/
>
> Institute for Computational Molecular Science
> Temple University, Philadelphia PA, USA.
>