VMD-L Mailing List

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Thu Mar 17 2011 - 05:16:04 CDT

Further, i don't know if autodock-vina takes residue names into
account, or only considers its (very raw) system of charges assigned.
Thus, if you come from charmm ff with residue names such as HSD, GLU
for either negatively charged or neutral glutamic acid, etc, how are
them treated. I did not check thus far.

I beg pardon for coming with pieces, which, however, come to mind
while I am now at autodock-vina with a charmm-ff (vmd-namd) derived
file.

This may be useful if you want to write the plugin for vmd.

First of all I had issues from ADT, which did not recognize
A:LYS95:HZ3 and C:ILE220:HG12 (sai these atoms have no bond, assigning
them zero charge), which have the same layout as those on other
chains, where they are recognized and assigned gesteiger. Second, ADT
misinterprets the first and last residue of each chain, such as
LEU1/LYS426, where it sees non-integral charge. I got the impression
(already time ago) that ADT is heavily buggy. I posed the question to
ADT developers, but they wanted my files, on which I work and i could
not. Proposing to provide a generic file with such problems was not
agreed.

f.

---------- Forwarded message ----------
From: Francesco Pietra <chiendarret_at_gmail.com>
Date: Thu, Mar 17, 2011 at 8:38 AM
Subject: Re: vmd-l: .pdbqt file type
To: nscerque_at_fc.up.pt, vmd-l_at_ks.uiuc.edu

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
>