AMBER Archive (2007)

Subject: AMBER: MM-PBSA problem: Why

From: jitrayut jitonnom (jitrayut.018_at_gmail.com)
Date: Sun Jan 21 2007 - 23:20:38 CST

Dear amber users,

I was wondering that this mmpbsa result below is OK ? Because i found
the E(inter) is zero at the final delta G (see below).

# COMPLEX RECEPTOR LIGAND
# ----------------------- -----------------------
-----------------------
# MEAN STD MEAN STD
MEAN STD
# ======================= =======================
=======================
ELE -6423.56 59.73 -6152.04 64.50
-178.10 6.83
VDW -789.19 24.69 -746.98 24.70
-2.73 2.65
INT 4728.01 43.38 4580.53 42.06
147.48 7.21
GAS -2484.74 65.62 -2318.49 69.22
-33.34 9.55
PBSUR 89.12 0.93 88.34 0.94
7.01 0.11
PBCAL -4061.25 51.67 -4046.86 54.31
-134.50 6.03
PBSOL -3972.13 51.63 -3958.52 54.22
-127.49 6.01
PBELE -10484.80 34.18 -10198.91 34.55
-312.59 3.12
PBTOT -6456.87 47.12 -6277.02 46.75
-160.83 6.54
GBSUR 89.12 0.93 88.34 0.94
7.01 0.11
GB -4161.91 52.40 -4142.02 56.13
-137.88 6.27
GBSOL -4072.79 52.45 -4053.68 56.15
-130.87 6.26
GBELE -10585.46 24.41 -10294.06 24.34
-315.98 2.89
GBTOT -6557.53 43.64 -6372.17 43.59
-164.22 6.57

# DELTA
# -----------------------
# MEAN STD
# =======================
ELE -93.42 12.78
VDW -39.48 2.75
INT 0.00 0.00 #######This line here indicate
some problem ?
GAS -132.90 12.69
PBSUR -6.23 0.44
PBCAL 120.11 11.31
PBSOL 113.88 11.17
PBELE 26.69 5.27
PBTOT -19.01 4.62
GBSUR -6.23 0.44
GB 117.99 11.61
GBSOL 111.77 11.48
GBELE 24.58 3.98
GBTOT -21.13 3.38

This one should i concern as a problem or it's ok. By the way, my
system is a enzyme-heptapeptide complex. For my opinion, this system
may indicate some problems for use this mm-pbsa method?

Any suggestions will be great.

Thank you in advanced,

Jitrayut
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