[AMBER] MMPBSA.py.MPI - Output discrepancies

From: George Tzotzos <gtzotzos.me.com>
Date: Tue, 04 Jan 2011 11:41:00 +0100

Happy New Year to all,

I've been running MMPBSA.py.MPI to determine Delta G for a protein-ligand. I've also run the program to determine per residue decomposition of entropy.

The same input files have been used in both cases. The the Delta G results obtained from Generalized Born differ by ~ 2kcal/mol

For example,

Differences (Complex - Receptor - Ligand):

DELTA G binding = -46.6213 +/- 3.1112 0.1663 (given by per-residue entropy decomposition)
DELTA G binding = -44.2279 +/- 2.7619 0.1476 (without per-residue entropy decomposition)

The same discrepancy of ~2kcal/mol has been observed using the same ligand with two (2) other receptors.

The Poisson Boltzmann calculations with and without per residue decomposition gave identical values

Differences (Complex - Receptor - Ligand):

 DELTA G binding = -34.0898 +/- 3.1112 0.1663

My specific questions are the following:

1. Is there an explanation for this discrepancy in the case of Generalized Born while this discrepancy is not observed in the Poisson Boltzmann calculations?

2. The Delta Gs given by the two methods are different by ~10 kcal/mol. That strikes me as being too much of a difference.

3. Is temperature (say 300K) factored in the ENTROPY calculations?

4. Can one assume that the enthalpy for the six translational and rotational degrees of freedom is 6*(1/2)*RT=1.8 kcal/mol at 300K?

Thanks in advance and best regards


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Received on Tue Jan 04 2011 - 03:00:03 PST
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