VMD-L Mailing List

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Wed Mar 16 2011 - 12:15:51 CDT

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