VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Mar 17 2011 - 09:56:08 CDT

Francesco,
  Thus far nobody has implemented a "pdbqt" reader for VMD.
My group doesn't really do docking (we do molecular dynamics)
and so we don't have much background with Autodock. Again, if
someone knows Autodock and its file formats quite well, I would
be happy to assist them with developing plugins to read and/or write
these files. These PDBQT files appear to be a modified version
of the PDB format, as described here:
  http://autodock.scripps.edu/faqs-help/faq/what-is-the-format-of-a-pdbqt-file

I can tell you with certainty that the existing PDB reader in VMD
will not like any of the special "ROOT", "BRANCH" and related records,
and they would be silently ignored by the existing VMD PDB plugin.

Cheers,
  John

On Wed, Mar 16, 2011 at 06:15:51PM +0100, Francesco Pietra wrote:
> Hello:
>
> Referring to John's answer:
>
> > Arneh,
> > We don't have a reader for Autodock's "pdbqt" format, but if
> > a lot of people would find it very useful to be able to load them
> > a pdbqt plugin could be written. Even better, if someone familiar
> > with pdbqt wants to write the plugin, I can give guidance and help
> > them get it done... :-)
> >
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> > On Thu, Jul 19, 2007
>
>
> may I ask if the matter was pursued? I am trying to examine vina
> (autodock-vina) results with vmd 1.9. Simple pdbqt files are opened,
> although options as to draw style are very limited. More complex
> cases, such as multimodel pdbqt files are not understood by vmd (in my
> hands).
>
> In the recent past, having fed vina with amber-derived files, I could
> do the task with chimera. Now, with namd(charmm.ff)-derived files used
> for vina, also chimera has problems, being able to show only one out
> of three subunits of the protein.
>
> As the planned work requires namd(charmm ff) simulations, it is vmd
> which would be preferable.
>
> Thanks
>
> francesco pietra 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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