AMBER Archive (2006)

Subject: AMBER: strange result of mm/pbsa

From: snowyowls (ethercui_at_gmail.com)
Date: Mon Jan 09 2006 - 22:43:11 CST

dear all amberusers:
i using mm_pbsa to caculate a complex trajrctory
the result is quit strange:
# COMPLEX RECEPTOR
LIGAND
# ----------------------- -----------------------
-----------------------
# MEAN STD MEAN STD
MEAN STD
# ======================= =======================
=======================
ELE -5587.59 1106.41 -5571.62 1187.84 75.14
88.32
VDW -1488.83 0.00 -1458.78 0.00 3169034.75
5169994.66
INT 10868723.21 6190738.40 10766213.90 6137258.97 104359.91
66801.31
GAS 10861646.79 6191365.34 10759183.50 6137859.27 3273469.79
5203479.94
PBSUR 96.91 16.22 97.02 15.80 2.52
0.19
PBCAL -7483.79 1964.05 -7526.92 1955.40 -176.05
91.50
PBSOL -7386.88 1949.94 -7429.90 1941.72 -173.53
91.37
PBELE -13071.38 1606.12 -13098.54 1621.61 -100.91
42.75
PBTOT 10854259.91 6189423.77 10751753.61 6135933.86 3273296.26
5203417.55
GBSUR 139.55 23.36 139.71 22.76 3.63
0.28
GB -8051.66 2011.03 -8031.16 1996.86 -197.88
96.45
GBSOL -7912.11 1990.14 -7891.44 1976.40 -194.25
96.24
GBELE -13639.25 1557.34 -13602.78 1597.88 -122.74
54.98
GBTOT 10853734.67 6189520.08 10751292.06 6136021.19 3273275.54
5203409.59

# DELTA
# -----------------------
# MEAN STD
# =======================
ELE -91.11 77.37
VDW -3169064.80 5169994.66
INT -1850.60 1045.05
GAS -3171006.51 5170373.49
PBSUR -2.63 0.71
PBCAL 219.19 164.61
PBSOL 216.55 164.25
PBELE 128.08 105.66
PBTOT -3170789.95 5170243.54
GBSUR -3.79 1.02
GB 177.37 108.65
GBSOL 173.58 108.28
GBELE 86.26 91.57
GBTOT -3170832.93 5170328.94

first the delta G is quit a large nagetive number
and then the std is quit a large number too

if I should run other tow md to create trajrctory of receptor and ligend
individual?

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