AMBER Archive (2009)

Subject: [AMBER] MM_PBSA problem in Amber 9

From: Sean Zhao (sean.r.zhao_at_gmail.com)
Date: Mon May 04 2009 - 04:09:14 CDT

Hello everyone,

  I used Amber 9 to simulate a small molecule bound in a protein. After I
have finished the MM_PBSA, I found the results ( shown below ) are very
unreasonable. How can I solve this issue? Any response will be appreciated.

By Sean

May 4, 2009

# COMPLEX RECEPTOR
LIGAND
# ----------------------- -----------------------
-----------------------
# MEAN STD MEAN STD
MEAN STD
# ======================= =======================
=======================
ELE -2681.36 122.08 -3421.88 124.66
204.62 6.22
VDW -553.61 24.44 10355220.28 12767.86 840207.22
1837.61
INT 3469.50 36.37 10058731.27 227704.56 395500.95
56455.11
GAS 234.53 135.56 20410529.66 227041.54 1235912.78
56454.41
PBSUR 74.89 2.18 73.69 1.80
3.99 0.12
PBCAL -1814.93 106.85 -3891.82 384.24
-295.13 9.74
PBSOL -1740.04 105.08 -3818.13 383.84
-291.14 9.71
PBELE -4496.29 24.58 -7313.70 400.80
-90.51 4.97
PBTOT -1505.51 45.78 20406711.53 226964.81 1235621.65
56447.36
GBSUR 74.89 2.18 73.69 1.80
3.99 0.12
GB -1838.70 110.06 -2844.96 71.25
-338.07 9.27
GBSOL -1763.80 108.31 -2771.27 70.84
-334.08 9.23
GBELE -4520.06 19.88 -6266.84 117.35
-133.46 4.90
GBTOT -1529.27 43.05 20407758.39 227023.61 1235578.70
56447.31
# DELTA
# -----------------------
# MEAN STD
# =======================
ELE 535.91 209.28
VDW -11195981.11 12895.21
INT -10450762.71 235940.50
GAS -21646207.91 234957.07
PBSUR -2.79 0.52
PBCAL 2372.01 369.52
PBSOL 2369.23 369.56
PBELE 2907.92 404.88
PBTOT -21643838.69 234929.04
GBSUR -2.79 0.52
GB 1344.33 109.99
GBSOL 1341.55 109.73
GBELE 1880.24 124.69
GBTOT -21644866.37 235008.21
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