When I used the hbond analysis in Simulation Event Analysis tool, I picked the hydrogen bond donor and acceptor atoms and the plot showed 0 hbonds although I am sure there is a hydrogen bond. What is wrong?

In Maestro, the hydrogen bond definition is based on the distance of the hbond but also acceptor and donor angles. In order to study the hydrogen bond between two functional groups you need to pick two atoms from each functional group. For example for this H-bond:

C=O.....H-O

you need to pick C, O, H, and O atoms.

Keywords: Simulation Event Analysis, hbond

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