ADL: H-bond donors and acceptors in Vina
edelmiro.moman at gmail.com
Sun Jun 14 03:11:24 PDT 2009
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):
Vina does not (based on the O-O distances, not only on the OH dihedrals).
However, Vina can identify this one:
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?
More information about the autodock