AMBER Archive (2004)

Subject: AMBER: Analysis mm_pbsa result

From: Xiao He (hx_at_itcc.nju.edu.cn)
Date: Fri Sep 24 2004 - 21:53:08 CDT

Here are my results and how to get the free energy of the ligand-acceptor system

1)binding
# COMPLEX RECEPTOR LIGAND
# ----------------------- ----------------------- -----------------------
# MEAN STD MEAN STD MEAN STD
# ======================= ======================= =======================
ELE -7741.60 30.85 -7355.18 30.79 -374.77 2.54
VDW -1341.17 29.36 -1311.00 29.12 16.93 1.75
INT 6587.63 37.20 6527.17 36.40 59.75 5.67
GAS -2495.14 36.07 -2139.02 33.83 -298.09 3.10
PBSUR 84.95 0.43 86.04 0.37 3.52 0.04
PBCAL -6186.86 271.26 -5610.83 41.09 -20.78 1.95
PBSOL -6101.91 270.94 -5524.78 41.07 -17.25 1.95
PBELE -13928.46 285.48 -12966.01 22.68 -395.55 3.51
PBTOT -8597.05 304.19 -7663.80 50.79 -315.35 2.89
GBSUR 122.33 0.62 123.90 0.54 5.07 0.05
GB -5513.21 36.99 -5520.72 35.53 -22.74 0.58
GBSOL -5390.88 37.09 -5396.81 35.64 -17.67 0.60
GBELE -13254.81 8.34 -12875.90 8.49 -397.51 2.68
GBTOT -7886.03 40.88 -7535.83 42.19 -315.76 3.00

# DELTA
# -----------------------
# MEAN STD
# =======================
ELE -11.64 2.64
VDW -47.10 1.67
INT 0.71 0.48
GAS -58.03 2.81
PBSUR -4.62 0.07
PBCAL -555.26 284.58
PBSOL -559.88 284.55
PBELE -566.90 286.01
PBTOT -617.91 285.92
GBSUR -6.65 0.10
GB 30.25 2.95
GBSOL 23.60 3.00
GBELE 18.60 1.13
GBTOT -34.43 1.69

2)nmode
# MEAN STD
# =======================
TSTRA 13.13 0.00
TSROT 11.05 0.01
TSVIB 34.27 0.49
TSTOT 58.45 0.50

In nmode it said

No skew or curtosis when zero variance in moment
No skew or curtosis when zero variance in moment

[1] Done mm_pbsa.pl mm_pbsa.in > mm_pbsa.log
                                 

　　　　　　　　Xiao He
　　　　　　　　hx_at_itcc.nju.edu.cn
　　　　　　　　　　2004-09-25

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