[Chimera-users] AutoVina Dock gives very different results running from GUI/command line tool

Mariana Assmann mariana.assmann at gmx.net
Mon Aug 13 06:25:07 PDT 2018

Hi everyone,

I am trying to do docking using the command line tool in chimera. I 
found that when I use the GUI opening Tools > Surface/Binding Analysis > 
AutoDock Vina and following the docking window, I get very similar 
results for the docking pose and score every time I run the docking. 
However, if I do the same with the command line tool (with the same 
parameters, box size, local version of vina, same dock prep), I get very 
different results: the ligand is never in a good docking position, 
always on a different side of the pocket, and sometimes even intercepts 
strands of the protein. The docking scores are also off.

I am using using Chimera 1.13 (build 41780), AutoDock Vina 1.1.2 (May 
11, 2011), and the following command line for docking:

vina docking receptor protein ligand #1.2 output 
/home/mariana/GTN/docking/keap1/docking_test13 search_center -7,3,-30.32 
search_size 19,21,21 backend local location /home/mariana/bin/vina 
num_modes 9

I also found that the command line does not accept any of the vina 
receptor or ligand options (e.g. receptor_addh) and gives me error 
messages when including those ("Keyword 'receptor_addh' doesn't match 
any known keywords")

Does anyone what the problems for those issues could be?

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