AMBER Archive (2008)

Subject: RE: AMBER: Problem with MMPBSA

From: Ray Luo (rayhuangluo_at_gmail.com)
Date: Mon Dec 08 2008 - 13:47:15 CST

Hi Daniel,

I can't understand why ... if possible, I'd like look at your two sets of
files. Please use, say, 10 snapshots in each case, to demonstrate the
differences.

All the best,
Ray

==========================================
Ray Luo, Ph.D.
Associate Professor
Dept Molecular Biology & Biochemistry
University of California, Irvine, CA 92697
USPS: PO Box 3900 Email: rluo_at_uci.edu
Phones: (949) 824-9528, 9562
Web: http://rayl0.bio.uci.edu/
==========================================

-----Original Message-----
From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
Daniel Emery
Sent: Monday, December 08, 2008 8:28 AM
To: amber_at_scripps.edu
Subject: AMBER: Problem with MMPBSA

Dear all,

I have a problem to calculate the binding energy between the biotin and
the streptavidin.
When I calculate the interaction energy between the biotin and a monomer
of the streptavidin, there is no problem. See the results below :

# DELTA
# -----------------------
# MEAN STD
# =======================
ELE -90.42 8.91
VDW -65.36 3.31
INT 0.00 0.00
GAS -155.79 8.68
PBSUR -8.18 0.16
PBCAL 109.32 7.51
PBSOL 101.14 7.52
PBELE 18.90 4.90
PBTOT -54.65 4.61
GBSUR -8.18 0.16
GB 107.08 6.91
GBSOL 98.90 6.93
GBELE 16.66 4.24
GBTOT -56.89 3.97

But, when I calculate the same interaction between the biotin and the
streptavidin in the tetrameric form, I have trouble with the result of
the PBSA calculation.
The result for the GBSA calculation looks OK but the PBSA results are so
different and the standard deviation is almost the same as the mean
result. See below:

# DELTA
# -----------------------
# MEAN STD
# =======================
ELE -72.87 11.04
VDW -62.17 4.68
INT -0.00 0.00
GAS -135.05 12.99
PBSUR -10.35 0.21
PBCAL -22.07 119.30
PBSOL -32.42 119.31
PBELE -94.94 117.26
PBTOT -167.46 116.31
GBSUR -10.35 0.21
GB 114.05 10.86
GBSOL 103.70 10.73
GBELE 41.18 4.29
GBTOT -31.34 5.77

The problem come from the electrostatic part of the GB calculation.
I use, in these 2 cases, the same (exept the atom definition) input for
the calculation of the binding energy.

With these informations, have somebody a explanation or have somebody
the same problem?
Have you an idea to fix it?

Thanks a lot for your help.

Regards,
Daniel 

-- 
EMERY Daniel
Ph.D. Student (Lab. R1)
Department of Organic Chemistry
University of Geneva
30, quai Ernest-Ansermet
CH-1211 Geneva 4
+41 22 379 61 55

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