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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Received on Wed Feb 14 2007 - 06:07:46 PST
