VMD-L Mailing List

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Thu Mar 17 2011 - 11:05:17 CDT

Hi John:
Another user has knowledge of the pdbqt format and, apparently, of tcl
language. I got private mail and, not noticing that it was to me, I
have answered today CC to VMD. You may have already noticed the
messages.

pdbqt format becomes tricky with organic molecules; in fact, VMD opens
pdbqt for proteins, not for organic molecules. Surely I would be happy
to help for what I can do.

I have just noticed that ADT (the gui to autodock and vina-autodock)
does not care about the amino acid residue name. HSP HIP, or even non
existent HSC, inserted by mistake, raised no warning by ADT and led to
the same results with VINA.

cheers
francesco

On Thu, Mar 17, 2011 at 4:10 PM, John Stone <johns_at_ks.uiuc.edu> wrote:
>
> Francesco,
>  I think the issue here is mainly that most of the people here are
> probably doing molecular dynamics and may not have expertise on Autodock
> or the file formats it uses.  Those of us not already familiar with Autodock
> are not likely to go out and learn it just to answer these questions.  What
> would make the most sense would be for you to supply some example files that
> you're having trouble working with, and then we have a starting point for
> discussion.  Up to now this discussion is all somewhat abstract since
> no files have been provided and there's lack of sufficient detail
> to understand your problems clearly.  Perhaps autodock experts would
> know exactly what you're talking about, but I am not such an expert.
>
> Cheers,
>  John Stone
>  vmd_at_ks.uiuc.edu
>
> On Thu, Mar 17, 2011 at 08:27:23AM +0100, Francesco Pietra wrote:
>> Hello:
>> Having had no reply to my question, I understand there is no interest
>> in VMD dealing with pdbqt files. However, I believe that docking can
>> hardly have any physical significance (if it has any at the current
>> state of the art, with docking "in vacuo" for a rigid-backbone
>> protein) without properly equilibrating the protein. To this concern,
>> I came across
>>
>> > well, but it is a field required by the PDB standard.
>> > if you check the definition of ATOM records in the PDB
>> > standard format documentation, only charge and sequence
>> > entries are named optional.
>> That's a good point. But, many modeling programs, including psfgen,
>> leaves the chain column blank by default.
>> I just think it would be more convenient if VMD didn't do anything to
>> PDB files except the things that I specifically tell it to do.
>> Sanghyun (year 2007)
>>
>> I was unable to trace any further comment on that. Therefore, may I
>> ask, after 4 years have elapsed, if vmd/namd-charmm.ff could be harmed
>> by conserving the subunit ID when preparing psf files? I was now using
>> namd/charmm.ff equilibrated pdf for autodock-vina and had to
>> reconstruct the chain ids to get pdbqt files.
>>
>> Autodock is of widespread use (perhaps too much for what it can do).
>> At any event, pdbdatabank has stopped to support segid, although
>> luckily it has not used its columns.
>>
>> thanks
>> francesco pietra
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
>  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078
>