ADL: Vina: Wrong H-bond networks

Mark Swingle mswingle at jaguar1.usouthal.edu
Sun Jun 7 11:00:47 PDT 2009


Miro,

As I recall from the Vina documentation, polar hydrogens are only used to type 
the heavy atoms they are bound to as either h-bond donors or h-bond 
acceptors. As far as Vina's scoring function is concerned, degrees of freedom 
that rotate hydroxyl groups are degenerate (i.e. all torsion angles are 
equivalent) and don't need to be set up as rotatable groups in the input 
files. Therefore, the torsion angles of such groups are basically random and 
meaningless in the output structures. However, Vina should be able to 
correctly position the hydroxyl oxygen. Your description suggests that is the 
case, yes? If so, I think your results are OK.

Regards,

Mark

On Sunday 07 June 2009 05:52:18 am Edelmiro Moman wrote:
> 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




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