Dear researcher,
I have calculated mm-pbsa for protein ligand complex. I considered only last 5 ns trajectory then i found these values.
van der Waal energy = -151.712 +/- 14.006 kJ/mol
Electrostattic energy = 331.642 +/- 29.645 kJ/mol
Polar solvation energy = -7560.146 +/- 1091.482 kJ/mol
SASA energy = -15.730 +/- 0.697 kJ/mol
SAV energy = 0.000 +/- 0.000 kJ/mol
WCA energy = 0.000 +/- 0.000 kJ/mol
Binding energy = -7395.945 +/- 1090.017 kJ/mol
But when i seleceted last 10 ns trajectory then value is
van der Waal energy = -156.555 +/- 14.641 kJ/mol
Electrostattic energy = -136.006 +/- 13.876 kJ/mol
Polar solvation energy = 306.060 +/- 14.317 kJ/mol
SASA energy = -15.630 +/- 0.666 kJ/mol
SAV energy = 0.000 +/- 0.000 kJ/mol
WCA energy = 0.000 +/- 0.000 kJ/mol
Binding energy = -2.132 +/- 14.836 kJ/mol
Why so much change in binding energy.
The binding energy of last 5 ns trajectory is correct or have some error.
please suggest me.
Check (visualize) the MD trajectory to explain these numbers. The differences are very large (HUGE): they should be visible to the naked eye . . . unless there is a problem in the energy calculation itself.
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If there is no dramatic change in the conformations of the protein and/or ligand, van der Waals (vdw) and electrostatic (ele) energies usually compensate each other, while their sum remains "constant" (with the standard deviation in low single digit kcal/mol or smaller). That is not your case though.
The polar solvation energy of -7,396 kJ/mol (-1,768 kcal/mol) is beyond extreme; it looks like some terms have not cancelled out . . .
Dear sir,
I saw the confirmation of our protein and ligand. The ligand is stable in the defined cavity till 50 ns simulation.
But i can not understand why this binding energy is so high.
This is not in acceptable range also.
The van der Waals energy term seems reasonable both in terms of quantity and stability. The problem is in the electrostatic energy terms ("electrostatic energy" and "polar solvation energy").
What are the numbers if you exclude the last 5 ns from the energy analysis?
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There seems to be a compensation of the two electrostatic terms, which makes sense. But their sum should not differ between the two parts of the MD trajectory much more than the van der Waals energy term . . .
I hope you have removed the PBC artefacts. See the stability of and other details of the simulation and make sure the system is stable.Which tool you used for mmpbsa calcualtions?
I used g_mmpbsa tools for analysis.
Link is following
http://rashmikumari.github.io/g_mmpbsa/
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