[Chimera-users] AutoDock Vina and hydrogens

Elaine Meng meng at cgl.ucsf.edu
Tue Apr 16 15:27:06 PDT 2013

Users of the AutoDock Vina interface in Chimera 1.7 should be aware of a potential "gotcha":  the structures should include hydrogens, at least the "polar" (potentially H-bonding) ones.  For the receptor, this is generally taken care of because the "add hydrogens in Chimera" option in the AutoDock Vina interface is turned on by default.  However, there is no corresponding option for the ligand in that interface: instead, you need to add hydrogens to the ligand beforehand, for example with Chimera AddH.  Polar hydrogens are needed for Vina to correctly recognize the atom types, to correctly calculate docking scores.  

In the current daily build (and for future releases) we have built in more protections so that if there are no hydrogens and you haven't added them with Chimera, they will still be added by the AutoDock prep scripts before the docking calculation.

Recent fixes:

Download the daily build:

Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

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