ADL: H-bond donors and acceptors in Vina

Edelmiro Moman edelmiro.moman at gmail.com
Sun Jun 14 03:11:24 PDT 2009


Hi,

I have already posted this question to the forum one week ago and I
obtained no answer (maybe because this post was mistaken with a
similar previous one).

>From some of our results with flexible side-chains, I have the
impression that a ligand hydroxyl group is labeled only as H-bond
donor, but not as an acceptor.

For instance, all other docking programs we have used so far,
including Autodock, do not
have any problem for identifying the following H-bond network (even if
the involved residues are flexible):

                  LIGAND
                        |
                     HO
                      /   \
TYROSINE-OH     HO-SERINE

Vina does not (based on the O-O distances, not only on the OH dihedrals).

However, Vina can identify this one:

                  LIGAND
                       =
                       O
                      /   \
TYROSINE-OH     HO-SERINE

So, yes if it is a carbonyl, no if it is a hydroxyl group.
Empirically, both should be efficient.

I have observed similar issues several times.

Can this be considered a "bug" or is it a random event?

Is there a way to manually label the
atoms as H-bond donor or acceptors or both?

Kind regards,

Miro



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