LIE protocol in QM/MM

From: Shahar Keinan (
Date: Fri Jan 03 2020 - 07:25:04 CST

Dear all,

I want to calculate the binding free energy (BFE) by the Linear
Interaction method (LIE) for a set of ligands with my protein of
interest using QM/MM energies. The binding free energy is estimated
based on the difference in the energetics of the interactions between
ligand and proteins in the “bound” versus “unbound” states.

So I need the Van der Waals interaction energies (VDW) and electrostatic
interaction energies (ELEC). These are the interaction energies between
the ligand (QM system) and water/protein (MM system).  For an only MM
system, this is not a problem, and can be done using the NAMDEnergy
window and collecting only the interaction energy.

The problem is that I can't find a way to collect only the interaction
energies in a QM/MM run. The NAMDEnergy tool don't seem to work for
QM/MM. Am I missing something?

Thank you for your suggestions.

Happy New Year,


Dr. Shahar Keinan
Chief Scientific Officer, Cloud Pharmaceuticals, Inc
Office: (984)-329-2388
Mobile: (919)-357-5319

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