AMBER Archive (2005)

Subject: AMBER: big fluctuation in MM-PBSA/GA

From: Eric Hu (eric.y.hu_at_gmail.com)
Date: Thu Apr 14 2005 - 17:54:05 CDT

Hi, I am doing a mm-pbsa/ga calculation on a peptide bound protein
complex. A 10ns simulation was performed at constant pressure after a
2ns simulation at constant volume.

 &cntrl
  imin=0,
  irest = 1,
  ntx = 7,
  ntb = 2, pres0 = 1.0, ntp = 1
  cut = 10,
  ntr = 0,
  ntc = 2,
  ntf = 2,
  tempi = 300.0
  temp0 = 300.0
  ntt = 3,gamma_ln = 1.0
  nstlim = 5000000, dt = 0.002
  ntpr = 1000, ntwx = 1000, ntwr = 1000
 /

A snapshot was taken every 2ps for binding energy calculation
(according to Tutorial_03). Here is the statistics.out.

# COMPLEX RECEPTOR LIGAND
# ----------------------- -----------------------
-----------------------
# MEAN STD MEAN STD
MEAN STD
# ======================= =======================
=======================
ELE -6255.77 74.88 -6116.28 70.61
-125.29 28.42
VDW -941.38 24.47 -899.06 23.11
-5.29 4.02
INT 4739.83 44.94 4525.88 43.84
213.94 9.19
GAS -2457.32 79.78 -2489.46 79.65
83.36 28.56
PBSUR 60.41 1.01 58.12 0.74
6.29 0.14
PBCAL -2428.13 69.47 -2336.18 60.15
-137.76 24.86
PBSOL -2367.72 69.00 -2278.06 59.78
-131.48 24.85
PBELE -8683.90 32.73 -8452.46 31.67
-263.05 5.04
PBTOT -4825.04 50.82 -4767.52 49.34
-48.12 9.49
GBSUR 86.99 1.45 83.69 1.07
9.05 0.21
GB -2294.84 68.98 -2207.64 64.40
-129.19 26.92
GBSOL -2207.85 68.42 -2123.95 63.92
-120.13 26.91
GBELE -8550.61 27.95 -8323.91 27.51
-254.48 3.78
GBTOT -4665.17 46.84 -4613.41 46.56
-36.78 9.05

# DELTA
# -----------------------
# MEAN STD
# =======================
ELE -14.20 28.32
VDW -37.03 7.62
INT 0.01 0.02
GAS -51.21 32.31
PBSUR -4.00 0.76
PBCAL 45.81 32.31
PBSOL 41.82 31.85
PBELE 31.61 9.06
PBTOT -9.40 6.93
GBSUR -5.75 1.10
GB 41.98 27.46
GBSOL 36.23 26.85
GBELE 27.79 4.27
GBTOT -14.99 7.54

The data here are not usable since the STD is bigger that the actual
value. I believe that the system is well equilibrated and wonder if
there are other ways to improve. Thanks.

Eric
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