AMBER Archive (2006)

Subject: AMBER: Semi-empirical parameterization -- van der Waals and H-bonding?

From: Evan Kelly (
Date: Mon Apr 03 2006 - 17:28:27 CDT


I am beginning a QM/MM study on a drug-protein interaction. Hydrogen
bonding and van der Waals forces are expected to be very important in
this system. My understanding is that AMBER has a QM/MM function
built into the SANDER module which treats the QM portion semi-
empirically. My question is then: does anyone know about the
parameterization of the semi-empirical methods? Mainly, are they
trained to handle H-bonding and van der Waals forces? Have there
been any studies done on AMBER's ability to treat QM/MM H-bonding, etc?


Evan Kelly

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