AMBER Archive (2007)

Subject: AMBER: Positive binding free energy!

From: Rima Chaudhuri (rima.chaudhuri_at_gmail.com)
Date: Tue Feb 13 2007 - 16:53:05 CST

Hi All,

I ran some mm_pbsa calculations, and am getting positive deltaG(bind) i.e.
the PBTOT = -30.69 and the TSTOT= -36.97, which is not possible, because the
Ki for the ligand is about 6nM. I am getting similar positive values for
some four other protein-ligand complexes. I saw a similar message posted,
but that was on a docked complex and might have had ligand conformation
problem. I am running the calculation on the MD performed on crystal
structures, using MM=1, PB=1, MS=1 over 100 snapshots from the last 200ps of
the 1ns simulation. I used 10 snapshots of those 100 for entropy
calculations. Any suggestions on what might have gone wrong? and what might
be a reasonable explanation..

# DELTA

# -----------------------

# MEAN STD

# =======================

ELE -64.04 14.86

VDW -60.27 3.27

INT -0.00 0.00

GAS -124.31 14.98

PBSUR -6.72 0.10

PBCAL 100.35 14.04

PBSOL 93.63 14.01

PBELE 36.30 4.41

PBTOT -30.69 4.46

# DELTA

# -----------------------

# MEAN STD

# =======================

TSTRA -13.43 0.00

TSROT -11.61 0.01

TSVIB -11.93 19.26

TSTOT -36.97 19.27

Thanks. 

-- 
-Rima

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