AMBER: MM_PBSA calculations

From: Jiten <jiten.postech.ac.kr>
Date: Thu, 30 Dec 2004 16:22:25 +0900

Dear Amber Users,

In one of my calculations using MM_PBSA for the free energy binding I got as follows

# COMPLEX RECEPTOR LIGAND
# ----------------------- ----------------------- -----------------------
# MEAN STD MEAN STD MEAN STD
# ======================= ======================= =======================
ELE -7752.61 116.71 -7610.76 118.55 -136.21 1.12
VDW -1496.47 24.26 -1450.63 24.42 12.29 2.02
INT 7058.42 38.36 6973.49 39.67 84.94 5.04
GAS -2190.66 116.33 -2087.90 119.84 -38.99 5.07
PBSUR 78.79 0.93 80.24 0.85 3.79 0.08
PBCAL -4283.36 109.31 -4301.42 125.96 -24.91 3.39
PBSOL -4204.56 108.59 -4221.18 125.40 -21.13 3.34
PBELE -12035.97 52.69 -11912.18 41.47 -161.13 3.25
PBTOT -6395.23 56.53 -6309.08 51.66 -60.11 5.96
GBSUR 113.46 1.33 115.55 1.23 5.45 0.11
GB -4321.06 106.83 -4319.64 107.78 -26.35 1.05
GBSOL -4207.60 105.86 -4204.09 106.88 -20.90 0.98
GBELE -12073.67 30.15 -11930.40 29.33 -162.56 1.08
GBTOT -6398.26 46.61 -6292.00 48.00 -59.88 5.21

# DELTA
# -----------------------
# MEAN STD
# =======================
ELE -5.64 4.19
VDW -58.13 2.56
INT 0.00 0.00
GAS -63.78 5.30
PBSUR -5.23 0.16
PBCAL 42.98 46.60
PBSOL 37.74 46.52
PBELE 37.34 45.90
PBTOT -26.03 44.22
GBSUR -7.54 0.23
GB 24.93 4.07
GBSOL 17.39 4.01
GBELE 19.29 1.96
GBTOT -46.38 2.08
~

Form the nmode

# MEAN STD
# =======================
TSTRA 13.30 0.00
TSROT 11.23 0.02
TSVIB 39.25 1.06
TSTOT 63.78 1.06

As the gas phase energy value and TSTOT al the same - I am worried about my result as there are some hydrogen bonds between the ligand and receptor. Can anyone suggest me how to interpret the data.

With best regards,


N. Jiten Singh
C/O Prof. Kwang S. Kim
Department of Chemistry
Pohang University of Science and Technology
San 31, Hyojadong, Namgu
Pohang 790-784, Korea
Phone : 82-54-279-5853 ( Lab ) / 279-4138 ( Appt )
Fax : 82-54-279-8137 (or +82-54-279-3399)
Web : http://csm.postech.ac.kr/ and http://www.postech.ac.kr/e
Home Page : http://www.geocities.com/njs_19

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Received on Thu Dec 30 2004 - 07:53:00 PST
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