ADL: Vina: Wrong H-bond networks

Edelmiro Moman edelmiro.moman at gmail.com
Sun Jun 7 03:52:18 PDT 2009


Hi,

I have been trying to reproduce some crystallographic complexes with
Autodock Vina. In terms of RMS, the results are very good. In terms of
scoring, they are not so good.

In a couple of cases, the hydrogen bond networks as identified by Vina are
obviously wrong. For instance, in one example with not flexibility in the
receptor and just one rotatable bond in the ligand (the one corresponding to
the dihedral angle of a hydroxyl group), every docking program (including
Autodock 3 and 4) finds the right solution for the H-bond network:

                              LIGAND
                                    |
                                 HO
                                /     \
 GLUTAMATE-C(O)-O-      HN-HISTIDINE

However, Vina finds this solution:


                              LIGAND
                                    |
                                 OH
                                      \
 GLUTAMATE-C(O)-O-      HN-HISTIDINE


So that the H of the ligand is pointing towards the H of the histidine.

I wonder how is this possible. Is Vina reading the polar hydrogens from the
pdbqt file or is it trying considering different protonation states?

Kind regards,

Miro

-- 
Edelmiro Moman, PhD
Pharmaceutical and Medicinal Chemistry
Saarland University
D-66041 Saarbrücken
Germany

Phone: +49 (0)681 302 70320 or 70328
Fax: +49 (0)681 302 4386

E-mail: edelmiro.moman at gmail.com
E-mail: e.moman at mx.uni-saarland.de

http://www.edelmiromoman.eu/


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