VMD-L Mailing List

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Thu Mar 17 2011 - 02:38:19 CDT

Hi Nuno:
your mail got misplaced in my system - and was therefore not noticed -
when i posted again on the subject. Sorry. The first step is having
the subunit ID conserved, which is not the case if one uses VMD/psf,
although it is easily reconstructed. As to chimera, the matter was
just blurred by ADT not working properly if there is no chain id. When
pdbqt file -even for multimodels - are correct, chimera does correctly
its job in reading pdbqt files. cheers francesco

On Thu, Mar 17, 2011 at 8:25 AM, Nuno Sousa Cerqueira <nscerque_at_fc.up.pt> wrote:
> hello
>
> i have experience in autodock and pdbqt.
> i would like to do such plug-in. any guidance is welcome
>
> Nuno M. F. Sousa A. Cerqueira
>
> Em 2011/03/16 17:57, "Francesco Pietra" <chiendarret_at_gmail.com> escreveu:
>
> 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
>