AMBER Archive (2008)

Subject: Re: AMBER: MM-PBSA and delphi

From: Navnit Kumar Mishra (
Date: Mon Jun 09 2008 - 04:05:38 CDT

Hello Neha;

I am appending some informations regarding you query about interaction
energy calculation.

Neha Gandhi wrote:

>Can I also use a single trajectory method in such case?
You can use single trajectory approach to compare the ligand affinity
against one receptor, however, if you would like to include the ligand
induced energy ( free energy of adaptation) which would be the
difference in the free energy between the holo and apo state of the
molecule, than you should use three separate trajectory approach.
deltaG(adopt) = < Gmmpbsa(holo) > - < Gmmpbsa(apo) >

The paper by Masukawa, et. al. /J. Med. Chem.,/ *46* (26), 5628 -5637,
2003. and /J. Am. Chem. Soc.,/ *128* (39), 12766 -12777, 2006. discused
it in detail.

>On Mon, Jun 9, 2008 at 1:49 PM, Neha Gandhi <> wrote:
>>Dear Amber users,
>>Can anybody tell me if I should use the final snapshots of the ligand,
>>receptor and complex to run the final MM-PBSA script along with
>>delphi? There is a conformational change in the complex.
As you know the sampling issue is one of the key point for accurate
binding energy calculation. So, the only one snapshot would not give you
the overall averaged interaction energy, however, in vivo experiment
overall conformational energy is measured. Thats why we use all the
conformations which sampled during the dynamics, and then we averaged it
to get <deltaE>. I would prefer to include all the conformations with a
frequency of 10 or 20 ps, I would leave the part of trajectory which is
not fully equillibriated.

with regards,

>>Neha Gandhi,
>>School of Biomedical Sciences,
>>Curtin University of Technology,
>>GPO Box U1987 Perth,
>>Western Australia 6845
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