VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Apr 12 2010 - 08:08:08 CDT

On Mon, 2010-04-12 at 13:38 +0200, Ajasja Ljubetič wrote:
> Yes, I have tried that, actually. But I get too many dihedrals (not
> just the IUPAC Chi1, Chi2 .. Chi4 but all possible dihedral angle

you get all the dihedrals that you feed VMD. like all _good_
programs, VMD does not make many assumptions about your data.
it just processes what you give it to work with and then it
is up to you to tell it how to trim it down. can you please
explain what you understand under IUPACK dihedrals?

if it is easy enough to implement, i could consider adding
a special case version for that. or even add some commands
to the high-level tools that allow to do the whole shebang.

> 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?

"unknown" refers to the force field type. in charmm class force field
this type is not stored in the topology file but inferred from the
atom type and the corresponding parameters are read from the parameter
file that you have to feed the simulation software. with 'topo
retypedihedrals' you can generate canonical dihedral types from
the atom types (note that those are canonicalized, i.e. not simple
the corresponding atom types concatenated. in other MD programs
dihedrals are identified with distinct type names or numbers and
thus VMD allows to store those.

hope that helps,
    axel.

> I'm using the 1.1 version of topotools. And I have loaded the molecule
> from a psf/pdb combination.
>
>
> Best regards,
> Ajasja Ljubetič
>
> 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 Ljubetič
> <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 Ljubetič
> > 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.
>
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com
http://sites.google.com/site/akohlmey/
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.