[Chimera-users] AutoVina Dock gives very different results running from GUI/command line tool
mariana.assmann at gmx.net
Mon Aug 13 06:25:07 PDT 2018
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
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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