AMBER Archive (2006)

Subject: Re: AMBER: Interaction Energy Calculation

From: Varsha Goyal (vgusp_at_yahoo.ca)
Date: Thu Nov 02 2006 - 17:04:12 CST

Thanks Vitor,
I looked at MM_PBSA and also the tutorial availaible
online but when I ran calculations I am getting very
huge standard deviation...I am not sure what could go
wrong.....can someone suggest me something...I cannot
think of anything.........

# COMPLEX RECEPTOR
             LIGAND
# -----------------------
----------------------- -----------------------
# MEAN STD MEAN
STD MEAN STD
# =======================
======================= =======================
ELE -6691.16 36.24 -6513.94
37.16 -127.49 2.28
VDW -1143.82 22.86 -1111.72
24.33 -1.09 0.69
INT 6480.90 31.62 6403.49
30.36 77.41 5.68
GAS -1354.07 27.51 -1222.17
27.89 -51.17 4.66
PBSUR 88.82 0.78 89.86
0.76 3.64 0.02
PBCAL -3146.73 1188.82 -3190.11
399.27 -33.71 1.69
PBSOL -3057.91 1188.91 -3100.24
398.90 -30.07 1.68
PBELE -9837.89 1200.93 -9704.05
401.48 -161.20 1.65
PBTOT -4411.98 1177.43 -4322.41
382.16 -81.24 4.64
GBSUR 88.82 0.78 89.86
0.76 3.64 0.02
GB -3135.38 36.82 -3149.87
37.26 -31.39 1.60
GBSOL -3046.56 36.42 -3060.00
36.87 -27.75 1.59
GBELE -9826.54 28.31 -9663.81
25.17 -158.88 1.67
GBTOT -4400.64 22.17 -4282.17
22.39 -78.92 4.85

# DELTA
# -----------------------
# MEAN STD
# =======================
ELE -49.72 7.80
VDW -31.01 4.40
INT -0.00 0.00
GAS -80.74 6.45
PBSUR -4.68 0.07
PBCAL 77.08 1003.69
PBSOL 72.40 1003.74
PBELE 27.36 1005.82
PBTOT -8.34 1006.52
GBSUR -4.68 0.07
GB 45.87 3.20
GBSOL 41.19 3.19
GBELE -3.85 5.23
GBTOT -39.55 4.44

Thanks in advance,
Varsha Gupta

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