VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri May 19 2006 - 15:28:44 CDT

Lubos,
  The FIELD file contains "molecules" which other programs might consider
to be chains. It's conceivable we could parse those FIELD molecules and treat
them as chains/segnames in VMD. The main problem I see with that is that
I didn't see anything in the DLPOLY documentation that relates the atom indices
of the CONFIG/HISTORY files with the atoms in the FIELD file, particularly
those that are in different "molecules" in the FIELD file. Any tips?

  John Stone
  vmd_at_ks.uiuc.edu

On Thu, May 18, 2006 at 09:40:41PM +0200, Mgr. Lubos Vrbka wrote:
> dear john,
>
> > As far as I know the DLPOLY HISTORY files don't contain chain information
> > in them. The current version of the DLPOLY plugin for VMD sets the chain
> > and segname information blank since it doesn't appear to be contained
> > in the HISTORY files. You'll either need to additionally load a PDB/PSF
> > or some other structure file that contains this information in order for
> > VMD to read it in.
> i think none of the vmd output files contain the chain/whatever
> information - dlpoly doesn't use no such properties.
>
> > If there are other DLPOLY file formats we should be
> > reading which provide this information, please let me know.
> regarding the last sentence - would it be possible to add support for
> DLPOLY CONFIG files? it's just the structure file, no trajectory. i
> think the full specs can be found at the dlpoly website (in the manual)
> - i attach a sample (not including velocities and forces):

[trimmed out]

>
> --
> .....................................................
> Mgr. Lubos Vrbka
>
> Center for Biomolecules and Complex Molecular Systems
> Institute of Organic Chemistry and Biochemistry
> Academy of Sciences of the Czech Republic
> Prague, Czech Republic
>
> http://www.molecular.cz/~vrbka
> ..................................................... 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078