VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu May 14 2009 - 20:59:20 CDT

Maxim,
  There aren't any automatic update features for the angles/dihedrals/etc
if you modify the bonding. At present, VMD merely carries the
angle/dihedral/etc information around but doesn't use it for anything
itself. You could update the angles etc yourself with some basic
scripting if you like, or you could run the structure through
autopsf/psfgen to regenerate the structure using more sophisticated
methods.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, May 14, 2009 at 09:01:40PM -0400, Maxim Paliy. wrote:
> Dear VMD experts
> I want to add a few bonds to my system (join two nucleic backbones)
> and then write the corresponding psf via e.g.
> set all [atomselect top all]
> $all writepsf my.psf
>
> The change in bonding is reflected this way, but the angles and
> dihedrals stay intact..
>
> How would I force the angles and dihedrals to update as well?
>
> For some reason, the simplest way
> readpsf 1.psf
> coordpdb 1.pdb
> readpsf 2.psf
> coordpdb 2.pdb
> writepsf my.psf
> writepdb my.pdb
> does not work for me (probably because the ends of the chains I want to
> join are not well aligned).
>
> maybe there are some other ways to accomplish this task without writing
> all psf file manually?
>
> Thanks a lot in advance for the suggestions,
> Maxim 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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