Re: LIE protocol in QM/MM

From: Marcelo C. R. Melo (
Date: Fri Jan 03 2020 - 11:26:04 CST

Hi Shahar,

Electrostatic interactions need special attention and treatment in QM/MM
simulations. They are either processed using specialized C/C++ code in the
QM module of NAMD (ComputeQM.C), or in wrapper scripts (python/bash/etc)
that call the QM code you are choosing to use. In either case, the
electrostatic interactions between all atoms in the QM region and all MM
partial charges from the surrounding region is calculated separately.
In your case, you could adapt a python script and use NAMD's QM/MM
interface to extract ligand-protein interactions for the region of
interest, and write them in a separate file.

VdW interactions between QM and MM regions are calculated in the same way
that two MM regions are calculated, so I don't believe there should be any
difference in the way they are reported.


On Fri, 3 Jan 2020 at 08:33, Shahar Keinan <>

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

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