Re: [AMBER] How to calculate the energy contributed by hydrogen bonds?

From: Jason Swails <jason.swails.gmail.com>
Date: Mon, 19 Mar 2012 22:27:01 -0400

Modern Amber force fields do not have an explicit hydrogen bond term (which is a 10-12 potential).

The decomposition of the energies into the various terms correspond directly to terms in the Amber force field plus a GB/PB solvation free energy term (and a non polar surface area term).

The contribution to the potential from the hydrogen bonds are part of the nonbonded interactions. The charge model of the Amber force field as well as other parameters are sufficient to capture this effect pretty well without the need for an additional term.

Therefore, there is no way to extract this information directly and any scheme to do so would be empirical and unrelated to the amber potential (I don't know of any schemes to do this, and MMPBSA.py certainly doesn't have a scheme to do this implemented).

HTH,
Jason

--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
On Mar 19, 2012, at 5:00 PM, bin wang <wang_p_z.yahoo.com.cn> wrote:
> Dear Amber users,
> 
> I am running a simulation to calculate binding free energy between a peptide and a small molecule.  I used MMPBSA.py to get the binding energy.  From the results I can see the electrostatic terms and nonpolar terms, but can I also get similar information for the contribution from hydrogen bonds?  
> Thank you for any suggestion.
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber

Received on Mon Mar 19 2012 - 19:30:02 PDT