Dear everyone
I am trying use mm_pbsa of Amber8 to calculate the free energy of
protein-peptide complex
but the results of PBSOL and PBCAL are negative values.
Here is my output files, especially the DELTA : the PBCAL and PBSOL
is negative
# COMPLEX RECEPTOR
LIGAND
# ----------------------- -----------------------
-----------------------
# MEAN STD MEAN STD MEAN
STD
# ======================= =======================
=======================
ELE -8819.26 81.68 -8270.79 73.29 -463.15
23.41
VDW -1597.84 28.15 -1518.95 26.69 -26.54
6.69
INT 8016.88 46.17 7600.80 40.58 416.08
13.63
GAS -2400.22 87.16 -2188.93 77.18 -73.62
24.31
PBSUR 102.85 0.93 97.33 0.86 12.68
0.19
PBCAL -5894.64 92.37 -5368.79 84.27 -479.58
16.26
PBSOL -5791.79 91.81 -5271.46 83.74 -466.90
16.17
PBELE -14713.90 38.77 -13639.57 36.54 -942.73
18.63
PBTOT -8192.01 41.32 -7460.39 38.02 -540.51
20.37
GBSUR 135.41 1.24 128.07 1.14 15.62
0.25
GB -4424.83 76.01 -3997.69 67.69 -537.64
20.92
GBSOL -4289.43 75.29 -3869.62 67.03 -522.01
20.84
GBELE -13244.09 26.08 -12268.48 24.63 -1000.79
6.23
GBTOT -6689.65 40.18 -6058.55 37.27 -595.63
12.28
#
DELTA
#
-----------------------
# MEAN
STD
#
=======================
ELE -85.33 10.21
VDW -52.35 3.82
INT -0.00 0.00
GAS -137.67 9.81
PBSUR -7.16 0.22
PBCAL -46.27 19.58
PBSOL -53.43 19.57
PBELE -131.60 15.41
PBTOT -191.10 15.28
GBSUR -8.29 0.30
GB 110.50 9.50
GBSOL 102.21 9.49
GBELE 25.17 2.34
GBTOT -35.47 3.01
I know the PBSOL is usually opsitive. Could you tell me how to correct
this interm?
Thank you very much
Best regards
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Received on Sun Apr 02 2006 - 06:10:05 PDT
