VMD-L Mailing List

From: Mgr. Lubos Vrbka (lubos.vrbka_at_uochb.cas.cz)
Date: Thu May 18 2006 - 14:40:41 CDT

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):

Shell water model - 0 waters

         0 2
         20.00000000 0.00000000 0.00000000
          0.00000000 20.00000000 0.00000000
          0.00000000 0.00000000 20.00000000
 Cu2 1
          0.00000000 0.00000000 0.00000000
 OW 2
         -9.90790253 -2.06607378 -2.09045693
 OWs 3
         -9.90790253 -2.06607378 -2.09045693
 HW 4
         -9.52154168 -2.94486569 -1.81035658
 HW 5
         -9.16725034 -1.42050195 -2.27667615
 OW 6
         -9.86839354 7.15368352 -8.41578964
 OWs 7
         -9.86839354 7.15368352 -8.41578964
 HW 8
          9.99407905 8.09893076 -8.11981715
 HW 9
         -8.91804260 6.88838734 -8.25313390
 OW 10
         -9.93405514 7.94102387 -3.48804990
 OWs 11
         -9.93405514 7.94102387 -3.48804990
 HW 12
         -9.21621244 7.41497743 -3.94409862
 HW 13
         -9.67364786 8.10517819 -2.53660630

it's necessary to convert it to history file in order to display it in
vmd and it's annoying. it would be very nice if you could add such
support in some of the future releases of vmd.

with best regards,
lubos 

-- 
.....................................................
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
.....................................................