Hi amber users,
I have a problem when I use mm_pbsa in amber 10 to calculate the binding energy of the complex. After docking using autodock 4.0, I chose a conformation of the ligand, which matched well with the crystal ligand in the complex, to do MD with the receptor, two structural waters were preserved. I got a sample of 4ns, a equilibrated system according to the RMSD of the backbone.
But the binding energy is abnormal:
# COMPLEX RECEPTOR LIGAND
# ----------------------- ----------------------- -----------------------
# MEAN STD MEAN STD MEAN STD
# ======================= ======================= =======================
ELE -8427.58 249.82 -7913.17 248.20 -504.26 14.77
VDW 21573827.80 32502.03 20373193.05 31945..80 1200511.78 3894.24
INT 7034641.54 60631.76 6982919.11 60080.98 51722.43 5624.52
GAS 28600041.76 67739.75 27348198.98 66677.44 1251729.96 7136.00
PBSUR 104.47 1.36 104.04 1.33 4.94 0.08
PBCAL -6167.49 140.62 -6144.17 142.81 -128.34 10.10
PBSOL -6063.02 140.19 -6040.13 142.34 -123.40 10.08
PBELE -14595.07 231.58 -14057.35 225.77 -632.60 14.24
PBTOT 28593978.74 67733.12 27342158.85 66668.31 1251606.56 7134.74
GBSUR 104.47 1.36 104.04 1.33 4.94 0.08
GB -7508.97 158.41 -7502.67 156.03 -108.80 8.85
GBSOL -7404.50 158.03 -7398.62 155.70 -103.86 8.83
GBELE -15936.55 195.91 -15415.84 191.87 -613.06 13.92
GBTOT 28592637.26 67731.79 27340800.36 66668.02 1251626.10 7134.65
# DELTA
# -----------------------
# MEAN STD
# =======================
ELE -10.15 18.22
VDW 122.97 158.98
INT 0.00 0.00
GAS 112.82 163.49
PBSUR -4.51 0.32
PBCAL 105.02 23.41
PBSOL 100.51 23.25
PBELE 94.88 17.49
PBTOT 213.33 157.50
GBSUR -4.51 0.32
GB 102.50 16.59
GBSOL 97.99 16.44
GBELE 92.35 11.01
GBTOT 210.81 159.42
The running of mm_pbsa is successful without any abnormal situation. What is the problem? And how can I figure it out? Any response will be highly appreciated!
All the best,
Qinghua Liao
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Aug 19 2009 - 20:30:43 PDT
