Dear all,
actually I did MM/PBSA ( using mm_pbsa.pl ) analysis of several systems
composed of one big molecule (receptor) and ligand which is composed of
several small and identical molecules (10 and 15) and in each case I have
obtained positive DELTA INT although I am using one-trajectory approach so
DELTA INT has to be zero.
One of such example is shown below. When I analyzed complexes where ligand
was composed just from one small molecule (1-1 complex), DELTA INT was
zero as should be.
I simply subtracted this positive DELTA INT from the final DELTA PB(GB)TOT
values to obtain correct dHs so I am
writing just to point to some potential bug in "INT" function ...
Best wishes,
Marek
PS: I am using Amber 11 with all bugfixes applied up to 12.
# COMPLEX RECEPTOR LIGAND
# ----------------------- -----------------------
-----------------------
# MEAN STD MEAN STD
MEAN STD
# ======================= =======================
=======================
ELE 7077.53 105.92 6914.25 45.36
512.15 83.00
VDW 1678.42 46.49 1808.87 43.51
9.53 10.05
INT 10680.81 58.33 9130.52 53.70
1436.64 20.26
GAS 19436.76 109.51 17853.64 54.83
1958.32 84.84
PBSUR 87.19 0.85 59.89 0.57
47.38 0.32
PBCAL -5253.41 92.04 -2065.72 36.00
-3629.95 78.55
PBSOL -5166.22 91.88 -2005.83 35.75
-3582.56 78.56
PBELE 1824.12 42.35 4848.54 32.27
-3117.80 12.42
PBTOT 14270.54 51.75 15847.81 44.46
-1624.25 20.15
# DELTA
# -----------------------
# MEAN STD
# =======================
ELE -348.87 48.06
VDW -139.98 9.38
INT 113.65 1.63
GAS -375.19 44.77
PBSUR -20.08 0.61
PBCAL 442.25 36.99
PBSOL 422.17 36.85
PBELE 93.39 22.67
PBTOT 46.98 17.39
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Received on Wed Feb 16 2011 - 12:00:08 PST
