Dear researcher
I have docked a compound with enzyme. It gives -5.4 Kcal/mol binding energy. Complex was stabilized by 5 Hydrogen bonds and many hydrophobic interaction. Then i have taken this complex for mm-pbsa calculation. Last 10 ns trajectory was taken for calculation. But it gives positive binding energy.
van der Waal energy = -29.368 +/- 18.231 kJ/mol
Electrostattic energy = 37.562 +/- 43.375 kJ/mol
Polar solvation energy = 184.969 +/- 93.717 kJ/mol
SASA energy = -4.597 +/- 3.005 kJ/mol
SAV energy = 0.000 +/- 0.000 kJ/mol
WCA energy = 0.000 +/- 0.000 kJ/mol
Binding energy = 188.567 +/- 43.495 kJ/mol
Why it gives positive energy. How can i solve this problem.
Well, I am not an expert in solvation problems, but I would not trust at all MM in delicate problems. Your result is evidently an artefact.
Hi Rohit,
why you only selected the last 10ns? you have to use the skip command in you MM/PBSA parameter file and used your complete trajectories for calculation. it will actually represent the whole system energy.
Dear Rohit
I agree with Andras, MM can not provide very accurate results in delicate problems. However, it offers an opportunity to measure the near accurate values. At this point I would suggest you to check the length and convergence of your trajectory. was it conversed ? further as MM - PBSA is not capable of calculating entropy contributions it always overestimates deltaG therefore you must take care of frames you are considering in pbsa calculation. usually 200 - 500 frames from a trajectory of 5ns are sufficient.
I have encountered similar problem when using g_mmpbsa. Apparently it was because of wrong indexing when choosing two groups for MMPBSA calculation. I would suggest to check the index file and see whether you use the correct groups in the calculation
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