Your internal energies are too high ... most likely your structures were
improperly generated. Try to visualize these snapshots first with the
matching prmtop files to see whether they are reasonable.
Ray
On Tue, May 22, 2012 at 7:41 PM, Khaled Barakat <kbarakat.ualberta.ca>wrote:
> 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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>
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Received on Wed May 23 2012 - 10:30:03 PDT
