[AMBER] atomic radii for PBSA

From: Qiong Zhang <qiong.zhang.qzh.gmail.com>
Date: Wed, 28 Dec 2011 17:58:49 +0100

Dear All amber users,

I am calculating protein-ligand binding affinity by MMPB(GB)SA approach
with MMPBSA.py in ambertools1.5. I would like to know the atomic radii set
to be used for PBSA.

In the manual, it is stated that mbondi2 radii set is optimized to be used
along with IGB2 and IGB5. How about PBSA please? Is it correct that the
Bondi radii set (set default PBRadii bondi) is for PBSA?

I did a little test with the same trajectory. The binding free energies
(without S,) for PB (GB) with different radii set are as follows:

mbondi2 GBSA(IGB2) G (-51.5626 kcal/mol)

mbondi2 PBSA G (-33.8270 kcal/mol)

bondi PBSA G (-31.2926 kcal/mol)

It seems that the PBSA results with bondi and mbondi2 radii set do not
differ a lot. If I'd like to compare GBSA(IGB2) and PBSA results, should I
use the same set of radii set please? If yes, does it mean that mbondi2
radii set should be used?

Thank you a lot in advance!

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Received on Wed Dec 28 2011 - 09:00:03 PST
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