Dear Amber users,
I have found some problems with the use the mmpbsa with only one molecule in
a 4 molecules group. I'm trying to evaluate the PBTOT, GBTOT of these four
ligants into specific protein receptor. I have the experimental values of
inhibition of these molecules and trying to find a theoretical reasons for
the observed experimental values, a correlation between them.
I did the minimization, heating and equilibration steps, plus eigth
nanoseconds of production step.
The extraction of the trajectories finish well so the pbsa calculations as
well. However, the results do not make any sense, because this molecule is
the most active and the results are
# COMPLEX RECEPTOR LIGAND
# ----------------------- -----------------------
-----------------------
# MEAN STD MEAN STD
MEAN STD
# ======================= =======================
=======================
ELE -2137.61 127.78 -2157.58 137.16
5.51 4.19
VDW 37496.55 890.89 -425.15 16.07 37908.73
917.73
INT 216395.38 38374.01 2486.23 25.44 213909.16
38348.57
GAS 251754.32 37610.91 -96.51 178.67 251823.40
37435.03
PBSUR 55.19 2.85 55.94 2.05
5.00 0.00
PBCAL -1626.14 80.34 -1583.37 135.71
-32.00 4.34
PBSOL -1570.94 77.48 -1527.43 133.66
-27.00 4.34
PBELE -3763.74 47.44 -3740.95 1.46
-26.49 0.15
PBTOT 250183.38 37533.42 -1623.93 45.02 251796.40
37430.68
GBSUR 55.19 2.85 55.94 2.05
5.00 0.00
GB -1645.95 123.22 -1621.38 137.00
-36.96 2.88
GBSOL -1590.75 120.36 -1565.44 134.95
-31.97 2.89
GBELE -3783.55 4.56 -3778.96 0.16
-31.46 1.30
GBTOT 250163.57 37490.54 -1661.95 43.72 251791.43
37432.14
# DELTA
# -----------------------
# MEAN STD
# =======================
ELE -7.01 4.43
VDW -40.49 3.07
INT 0.00 0.00
GAS -47.51 5.47
PBSUR -5.72 0.15
PBCAL 31.13 7.64
PBSOL 25.41 7.57
PBELE 24.12 5.57
PBTOT -22.10 4.47
GBSUR -5.72 0.15
GB 21.52 5.00
GBSOL 15.80 4.95
GBELE 14.50 2.37
GBTOT -31.71 2.45
Well, I do not have any ideas for the reason of this behaviour, so any
answer is very welcome!!!!!
Thank you very much!!
Prof. Dr. Moacyr Comar Junior
Universidade Federal de São João del Rei
Campus Centro-Oeste
Divinópolis - MG
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Received on Tue Feb 22 2011 - 05:30:04 PST
