Hi All,
I'm performing MMPBSA analysis for a protein-ligand complex. The ligand is
a nucleotide analogue that is the substrate for the protein (an enzyme).
The active site includes two magnesium ions that are coordinated by the
oxygens of the phosphate groups of the nucleotide along with three protein
residues. I did a 2ns MD simulation after minimizing the solvated system
for 100,0000 steps, heating it to 310, equilibrating it for 100 ps. From
the 2 ns I extracted snapshots for MMPBSA calculation using AMBER10. I used
99SB FF for the protein and GAFF for the nucleotide.
I'm getting very high electrostatic energy (see below) compared to many
problems that I have used MMPBSA to solve for before (but no metal ions
were present). Is that a normal situation due to the presence of the metal
ions or do I miss something?
Your guidance and help is so much appreciated,
Best regards,
Khaled
MMPBSA output --------
# COMPLEX RECEPTOR LIGAND
# ----------------------- -----------------------
-----------------------
# MEAN STD MEAN STD MEAN
STD
# ======================= =======================
=======================
ELE -17091.64 87.97 -13952.48 90.05 -517.53
12.78
VDW -2407.41 35.55 -2438.14 32.47 20.90
4.32
INT 12374.38 82.04 12088.00 79.50 286.38
11.66
GAS -7124.67 100.05 -4302.63 105.01 -210.25
11.05
GBSUR 173.24 0.99 174.42 1.01 4.00
0.07
GB -7843.93 83.25 -9370.54 92.60 -755.72
9.36
GBSOL -7670.69 83.31 -9196.12 92.62 -751.71
9.33
GBELE -24935.57 36.31 -23323.03 30.22 -1273.25
9.56
GBTOT -14795.37 64.92 -13498.75 64.25 -961.97
8.26
# DELTA
# -----------------------
# MEAN STD
# =======================
ELE -2621.63 35.15
VDW 9.84 7.58
INT 0.00 0.00
GAS -2611.79 34.99
GBSUR -5.19 0.17
GB 2282.33 36.81
GBSOL 2277.14 36.72
GBELE -339.30 14.74
GBTOT -334.65 10.64
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Received on Tue May 22 2012 - 20:00:04 PDT
