Re: [AMBER] Binding Energy Calculation by QM/MM method

From: Billy Miller III <>
Date: Sun, 14 Mar 2010 09:40:19 -0500

There is currently no working version of QM/MMGBSA to calculate the binding
free energy in AMBER, although efforts are currently underway to include
this implementation. A way for you to get around this would be to setup the
unsolvated complex, receptor, and ligand mdcrds yourself, and then run a
QM/MM using sander and set imin=5 to do a post-processing analysis on all
three of those trajectories. You can grep out the energies and do the
statistics analysis yourself, also.

There are a lot of reference papers regarding QM/MMGBSA out there. Here are
just a few of those references:
1. Massova and Kollman. *Perspectives in Drug Discovery and Design*. 2004.
2. Raha and Merz. *JACS*. 2004.
3. Grater, *et al. J Phys Chem B*. 2005.

I hope this helps!

-Bill Miller III

On Sun, Mar 14, 2010 at 12:45 AM, Kshatresh Dutta Dubey <
> wrote:

> Dear All
> I have done QM/MM Calculations of a protein ligand complex Using
> Amber10. I want to calculate binding energy of the ligand with protein
> using QM/MM method. Is there any method to calculate it? If yes , then
> how? Kindly give me some reference papers regarding to this method.
> Thanks in advance.
> Regards
> Kshatresh Dutta Dubey
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Received on Sun Mar 14 2010 - 08:00:02 PDT
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