[Chimera-users] Looking at docked data with the receptor shows as surface

Jonathan Y Wang wang.ying.jonathan at utexas.edu
Mon Mar 20 10:56:18 PDT 2017

Thank you so much for your help and your timely response! I appreciated how
clear your explanations were and your thoughts on how each might've

Have a blessed day,
Jonathan Wang

On Mar 20, 2017 12:52 PM, "Elaine Meng" <meng at cgl.ucsf.edu> wrote:

> Hi Jonathan,
> Autodock Vina and the Autodock prep scripts it calls were developed by a
> different group, and Chimera just communicates with a web service to run
> the docking part.  Thus I’m not an authority on the program, and for
> details you should probably consult the Autodock Vina website, publication,
> or its developers:
> <http://vina.scripps.edu/>
> <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3041641/>
> Nevertheless, here are some thoughts as to how it works and what you
> should check.
> As I understand it, AutoDock Vina does not use the surface per se, but it
> takes into account the (nonhydrogen) receptor atoms, and should not give a
> good score when ligand atoms are too close to receptor atoms.
> One thought is that maybe although the structure you are viewing is a
> trimer, what was returned by the receptor-prep script and actually used in
> the docking calculation was some smaller set of atoms, such as only the
> monomer.  If you entered “/location/name” as the output file in the Chimera
> dialog, then this prepared receptor file would be
> /location/name.receptor.pdbqt.  You should open this file in Chimera, and
> verify that it contains the receptor atoms you expected.  (I do not know if
> this prep script handles multimers correctly.)
> From the Chimera manual page <http://www.rbvi.ucsf.edu/chimera/docs/
> ContributedSoftware/vina/vina.html> :
> Output file - location and filename prefix for output files. If the prefix
> is name, the files generated by a successful run will be:
>         • name (or name.pdbqt if indicated in the file browser) - docking
> results in PDBQT format...
>         • name.receptor.pdb - receptor PDB file from Chimera, input to the
> AutoDock receptor preparation script
>         • name.receptor.pdbqt - processed receptor in PDBQT format, input
> to AutoDock Vina
>         • name.ligand.pdb - ligand PDB file from Chimera, input to the
> AutoDock ligand preparation script
>         • name.ligand.pdbqt - processed ligand in PDBQT format, input to
> AutoDock Vina
>         • name.conf - AutoDock Vina configuration file
> Another thought is that the calculation failed to find any positions of
> the ligand and it is just in the original position as input to docking.
> However, this would probably be fairly obvious.
> I hope this helps,
> Elaine
> ----------
> Elaine C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> > On Mar 20, 2017, at 12:30 AM, Jonathan Y Wang <
> wang.ying.jonathan at utexas.edu> wrote:
> >
> > To whom it may concern,
> >
> > Hi! I recently docked a ligand onto a receptor using the AutodockVina
> tool and when I opened the data the ligand seemed to be placed in the
> middle of the trimer. I showed the receptor as surface and it seems as if
> the ligand is too big to fit inside any of the holes surrounding the
> trimer, but somehow it has placed itself inside. I additionally opened it
> using PyMol to double check the file, but it also seems too small to fit
> inside any of the holes.
> >
> > My inquiry is this: Does AutodockVina take into account surface
> projections when performing docking?
> >
> > Thank you so much for your time,
> > Jonathan Wang
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