[Chimera-users] Problem with autodock vina in chimera

Don Gabo gabrielsrbio at gmail.com
Fri Jan 17 17:39:51 PST 2020

Also recently I'm having trouble, I was using AutoDock Vina just fine last
month and this week I started using it and I have to repeat the dcking
procedure twice coz' the first one doesnt wok, also the docking result is
all wrong, not what it used to be. Would it be a matter of Software

On Fri, Jan 17, 2020 at 6:51 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Also, it sounds like you might have been looking at the ligand pdbqt file
> (which is created so that it can be used as input to the docking step), not
> the docking results pdbqt file.  The different pdbqt files are described in
> the manual page under “Output file”:
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html>
> Elaine
> > On Jan 17, 2020, at 3:19 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> >
> > Hi,
> > I tried Chimera’s Autodock Vina interface to the web service twice today
> after you sent this message as a bug report, I do not see this problem: it
> returned results to me normally.
> >
> > When results are available, Viewdock starts automatically and shows the
> results; you would not need to start it yourself.  I do not get any message
> about a results directory.  Tested using a recent version of Chimera.  If I
> show the Reply Log (open from Favorites menu) it says something like this
> when the calculation finishes:
> >
> > Job 669753 exited with exit code 0.
> >
> > It may be that even though the calculation finished, because of your
> specific structures and choices of input parameter values, there are zero
> results. Or, you did not wait long enough for the calculation to finish and
> they were not yet written to the pdbqt file even though that file existed.
> >
> > However, importantly, you should be aware that this docking web service
> only allows very little sampling and is not suitable for most research
> purposes, as stated in the boxed warning on the manual page:
> > <
> http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html>
> >
> > I hope this helps,
> > Elaine
> > -----
> > Elaine C. Meng, Ph.D.
> > UCSF Chimera(X) team
> > Department of Pharmaceutical Chemistry
> > University of California, San Francisco
> >
> >
> >> On Jan 16, 2020, at 10:00 AM, De campos, Luana J <
> luana.decampos at unmc.edu> wrote:
> >>
> >> Hi,
> >> I am using the option autodocking vina in chimera and I have a problem
> related to the docking results. I set up the docking parameters all correct
> and initiate the docking run. Apparently, everything goes well, I even
> receive a message in chimera saying that I can see the results in the
> directory chosen. However, when I use the option "ViewDock" I can not see
> the results and I get I message saying that the file .pdbt does not appear
> to be dock out. Also, the docking calculation goes really fast, not like
> before that I used to take some time. In my inspection of the .pdbqt file
> created in the directory from the docking calculation (using note pad) it
> just has the compounds and the flexible bonds, it does not have the
> energies of the complexes ligand-protein.
> >> Is there any way to correct this bug?
> >> Thank you very much.
> >> Luana de Campos
> >> Pharmaceutical sciences PhD. student
> >> University of Nebraska Medical Center
> >
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