Dear Sir,
When I use mm_pbsa to calculate the binding energy, I obtained one abnormal results. The binding free energy is -6563.33 and -6566.00 from mm_pbsa and mm_gbsa, respectively. The detailed results were given as follows. From the analysis of obtained results, I found there are some problems of the calculation of VDW interaction. But for another system, I can obtain the correct results. I don't know what will result in this phenomenon. Could you give me some sugestions? Thanks a lot!
Best regards
Sincerely yours
Xiang
# COMPLEX RECEPTOR LIGAND
# ----------------------- ----------------------- -----------------------
# MEAN STD MEAN STD MEAN STD
# ======================= ======================= =======================
ELE -10198.84 73.96 -9459.89 70.48 -398.67 9.87
VDW -1828.25 30.59 4686.12 600.89 9.12 3.33
INT 8237.13 53.79 8105.42 52.94 100.66 8.49
GAS -3789.97 83.19 3331.66 608.29 -288.88 7.11
PBSUR 104.27 0.99 105.32 0.95 3.88 0.03
PBCAL -2814.21 55.59 -2927.07 53.21 -161.48 4.27
PBSOL -2709.94 55.29 -2821.75 52.87 -157.60 4.26
PBELE -13013.05 38.02 -12386.96 36.75 -560.15 8.98
PBTOT -6499.91 56.38 509.90 605.51 -446.48 4.76
GBSUR 104.27 0.99 105.32 0.95 3.88 0.03
GB -2966.35 58.43 -3084.64 56.22 -153.39 4.24
GBSOL -2862.08 58.13 -2979.32 55.87 -149.51 4.23
GBELE -13165.19 32.04 -12544.53 29.95 -552.05 8.19
GBTOT -6652.05 55.03 352.34 604.65 -438.39 4.97
# DELTA
# -----------------------
# MEAN STD
# =======================
ELE -340.29 19.99
VDW -6523.49 601.43
INT 31.04 2.55
GAS -6832.74 601.79
PBSUR -4.93 0.12
PBCAL 274.34 13.02
PBSOL 269.41 13.06
PBELE -65.95 10.28
PBTOT -6563.33 600.87
GBSUR -4.93 0.12
GB 271.67 12.90
GBSOL 266.74 12.95
GBELE -68.62 9.87
GBTOT -6566.00 601.10
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Received on Mon Oct 05 2009 - 20:00:02 PDT
