Dear Amber users:
The MM-PBSA module is a useful and convenient tool for binding free energy estimation. Most of the time, we are only interested in the
statistics.out file in which the raw data in the all.out files have been processed.
However, I find some problem in understanding the energy terms in the all.out files. Especially in the PBSA
part.
For example:
this is part of complex.all.out file
1
BOND = 567.9734 ANGLE = 1437.4321 DIHED = 1887.1406
VDWAALS = -1483.4718 EEL = -13040.5101 EGB = -2288.8782
1-4 VDW = 647.3136 1-4 EEL = 7412.2126 RESTRAINT = 0.0000
corrected reaction field energy: -3742.757259
surface area = 9173.513
ECAVITY = 9173.513
EDISPER = 0.0000
and this is the statistics.out file
COMPLEX RECEPTOR LIGAND
# ----------------------- ----------------------- -----------------------
# MEAN STD MEAN STD MEAN STD
# ======================= ======================= =======================
ELE -5568.72 60.24 -5451.55 60.52 -76.46 1.34
VDW -801.05 19.56 -744.16 19.14 7.41 2.22
INT 3895.25 37.19 3802.19 36.23 93.06 6.04
GAS -2474.52 72.66 -2393.52 71.95 24.01 5.94
PBSUR 66.15 0.85 67.34 0.88 7.02 0.06
PBCAL -2306.19 56.90 -2330.92 57.44 -39.45 0.80
PBSOL -2240.05 56.53 -2263.58 57.09 -32.42 0.79
PBELE -7874.91 21.07 -7782.47 21.34 -115.91 1.21
PBTOT -4714.57 37.75 -4657.10 36.41 -8.41 5.79
GBSUR 66.15 0.85 67.34 0.88 7.02 0.06
GB -2353.39 59.16 -2367.57 59.10 -41.49 0.95
GBSOL -2287.25 58.81 -2300.23 58.77 -34.47 0.93
GBELE -7922.11 19.05 -7819.12 19.33 -117.96 1.21
GBTOT -4761.76 36.98 -4693.75 35.94 -10.46 5.80
# DELTA
# -----------------------
# MEAN STD
# =======================
ELE -40.70 4.75
VDW -64.31 3.63
INT 0.00 0.00
GAS -105.01 5.83
PBSUR -8.22 0.37
PBCAL 64.17 3.78
PBSOL 55.95 3.65
PBELE 23.47 3.74
PBTOT -49.06 4.24
GBSUR -8.22 0.37
GB 55.67 3.71
GBSOL 47.45 3.57
GBELE 14.97 3.38
GBTOT -57.56 3.95
As I am quite unfamiliar with the equations in the PB and SA analyses,
Could anyone kindly explain how to converse the corrected reaction field energy and surface area into PBCAL and PBSUR???
Best Regards!
Xiaonan Zhang
Shanghai Public Health Clinical Center
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Mar 13 2009 - 01:17:21 PDT
