AMBER Archive (2009)

Subject: [AMBER] Non-zero internal energy in single trajectory MM-PBSA calculations

From: Dmitry Osolodkin (divanych_at_rambler.ru)
Date: Mon May 04 2009 - 04:24:59 CDT

Dear all,

When performing a MM-PBSA analysis of a trajectory, I get a strange
result. It is mentioned in the tutorial that during the single
trajectory analysis deltaEint must be zero, but I get INT = 277 kcal/mol
(see attached file). Difference between GBTOT and INT is reasonable, and
as I understand, deltaGbind = GBTOT - INT = -21 kcal/mol. What can be
the reason for such a problem? Should I concern about usage of these
results?

Best regards,
Dmitry 

-- 
Dmitry Osolodkin
Researcher
Group of Computational Molecular Design
Department of Chemistry
Moscow State University
Moscow 119991 Russia
e-mail: dmitry_o_at_org.chem.msu.su
Phone: +7-495-9393557
Fax: +7-495-9390290

# COMPLEX RECEPTOR LIGAND
# ----------------------- ----------------------- -----------------------
# MEAN STD MEAN STD MEAN STD
# ======================= ======================= =======================
ELE -11339.48 121.36 -11302.11 122.12 -33.78 2.47
VDW -1469.43 35.66 -1453.58 31.85 19.61 3.29
INT 7942.46 55.87 7506.24 56.44 159.01 6.94
GAS -4866.44 120.85 -5249.44 125.98 144.84 6.53
PBSUR 132.70 1.79 132.01 1.43 5.73 0.03
PBCAL -4146.16 97.55 -4156.57 101.15 -20.15 0.75
PBSOL -4013.46 97.58 -4024.56 100.94 -14.43 0.75
PBELE -15485.64 41.17 -15458.68 40.05 -53.94 2.31
PBTOT -8879.90 59.08 -9274.00 59.63 130.41 6.48
GBSUR 132.70 1.79 132.01 1.43 5.73 0.03
GB -4188.32 101.64 -4196.13 103.13 -11.59 0.94
GBSOL -4055.62 101.76 -4064.11 102.97 -5.87 0.93
GBELE -15527.80 33.47 -15498.23 33.05 -45.38 2.77
GBTOT -8922.06 56.86 -9313.56 56.68 138.97 6.52

# DELTA
# -----------------------
# MEAN STD
# =======================
ELE -3.59 4.62
VDW -35.45 8.16
INT 277.21 8.13
GAS 238.16 13.66
PBSUR -5.04 0.75
PBCAL 30.56 8.44
PBSOL 25.52 7.85
PBELE 26.97 7.65
PBTOT 263.69 9.60
GBSUR -5.04 0.75
GB 19.40 4.96
GBSOL 14.36 4.72
GBELE 15.81 2.33
GBTOT 252.53 11.93


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