High positive van der Waal energy and binding energy

[fateme....@gmail.com]

Hi

I have performed several protein-ligand MD simulations, for two of them, I got highly positive Van der Waal and binding energy.

The charge of the protein is zero and I did not add any ions.

The time of MD simulation is 400 ns, and I took the last 50 ns of simulation.

I did not change any option of pbsa.pdb. 

During simulation I have just changed the dt to 1 ft because of one molecule.

I don't know where is the problem and how to correct.

regards

[hassan rasouli]

When you sometimes conduct an MD simulation with poorly optimized ligands, the calculated energies may not be matched with traditional values. To correct this, please divide your MD simulations into different time intervals, try splitting your MD outputs for each step, and recalculate the energies. You should also check the chemical structure of your ligands before molecular docking simulation. Indeed, the quality of the docking procedure is another determinant factor that can affect the content of calculated energies for your complexes. In this case, you should check the grid box coordination, the vicinity of catalytic residues to backbone atoms of your ligand, etc. 

Regards,