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From: bin wang <wang_p_z.yahoo.com.cn>

Date: Tue, 20 Mar 2012 22:17:29 +0800 (CST)

Thank you very much.

So can we say the "Electrostatic" term in the energy decomposition include the contribution from hydrogen bonds? I am just thinking maybe we can use the energy decomposition to see which residues or pairs have hydrogen bonds and contribute most to the total binding energy. If this is not the right way to do it, how should I explain the decomposition results?

BTW, I found that the sum of total energy of each residue is not equal to the energy change of the "DELTA G binding" without decomposition. Could you let me know if the decomposition is a weighted summary or some special algorithm is used here?

________________________________

From: Jason Swails <jason.swails.gmail.com>

To: bin wang <wang_p_z.yahoo.com.cn>; AMBER Mailing List <amber.ambermd.org>

Sent: Monday, March 19, 2012 10:27 PM

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

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

Date: Tue, 20 Mar 2012 22:17:29 +0800 (CST)

Thank you very much.

So can we say the "Electrostatic" term in the energy decomposition include the contribution from hydrogen bonds? I am just thinking maybe we can use the energy decomposition to see which residues or pairs have hydrogen bonds and contribute most to the total binding energy. If this is not the right way to do it, how should I explain the decomposition results?

BTW, I found that the sum of total energy of each residue is not equal to the energy change of the "DELTA G binding" without decomposition. Could you let me know if the decomposition is a weighted summary or some special algorithm is used here?

________________________________

From: Jason Swails <jason.swails.gmail.com>

To: bin wang <wang_p_z.yahoo.com.cn>; AMBER Mailing List <amber.ambermd.org>

Sent: Monday, March 19, 2012 10:27 PM

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

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 _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Tue Mar 20 2012 - 07:30:02 PDT

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