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

[Elaine Meng]

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