AMBER Archive (2009)

Subject: [AMBER] Error in binding energy (MM PBSA)

From: Vikas Sharma (vs_vikassharma_at_yahoo.co.in)
Date: Thu May 07 2009 - 00:47:33 CDT

Dear All,

I am using Amber10..
i used MM PBSA for binding free energy calculation...
I used antechamber (AM1 BCC charges)...i performed a 1 ns simulation with 1 fs time step...
after production MD i extracted the co-ordinates and then calculated free enrgy using MM PBSA...i am getting delta PBTOT as a positive value...

how can i correct this?

thanks

i am pasting the entire snapshots_statistics.out file below:

# COMPLEX RECEPTOR LIGAND
# -----------------------
----------------------- -----------------------
# MEAN STD MEAN STD MEAN STD
# =======================
======================= =======================
ELE 207245.25 648.49 -2589.11 114.91 218694.23 300.55
VDW -225.23 25.41 -631.86 19.68 -1.21 0.01
INT 12998.79 75.87 5802.95 58.20 7195.84 42.13
GAS 220018.81 618.06 2581.98 140.77 225888.86 267.56
PBSUR 120.47 2.52 116.64 2.52 7.53 0.01
PBCAL -425032.07 703.46 -5251.30 97.38 -432908.62 382.61
PBSOL -424911.60 701.91 -5134.65 97.84 -432901.09 382.62
PBELE -217786.82 148.07 -7840.41 43.20 -214214.39 134.67
PBTOT -204892.80 179.47 -2552.68 73.82 -207012.23 161.70
GBSUR 120.47 2.52 116.64 2.52 7.53 0.01
GB -429296.07 680.15 -5298.08 102.48 -438823.22 369.02
GBSOL -429175.60 678.63 -5181.44 103.27 -438815.68 369.02
GBELE -222050.81 107.43 -7887.19 27.49 -220128.99 98.09
GBTOT -209156.79 149.13 -2599.46 63.32 -212926.83 133.98

# DELTA
# -----------------------
# MEAN STD
# =======================
ELE -8859.86 534.46
VDW 407.84 18.83
INT -0.00 0.00
GAS -8452.03 533.35
PBSUR -3.71 0.03
PBCAL 13127.85 536.96
PBSOL 13124.14 536.97
PBELE 4267.98 92.63
PBTOT 4672.11 90.50
GBSUR -3.71 0.03
GB 14825.23 529.57
GBSOL 14821.52 529.57
GBELE 5965.37 73.72
GBTOT 6369.50 80.51

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