Dear All,
I have performed a series of electrostatic calculations on MD trajectories
for a macromolecular complex using APBS, and I have recorded at each time
step (every 10 ps for a total simulated time of 50 ns) the electrostatic
binding energy for the complex formation, obtained by subtracting the
electrostatic binding energies of the single binding partners from the
electrostatic binding energy of the complex.
With the help of a little script I have then plotted the electrostatic
binding energy as a function of the simulated time.
Overall, I get a nice profile that corresponds to what I expected. However,
along the simulated time the graph is spiky. At some time steps the energy
drops suddenly down (I would expect a little spike but not a variations of a
couple of orders of magnitude). Can you please help me to understand why
this happens? Can this be due to the fact that the change in conformation of
the ligand and/or target has as an effect the neutralization of some charges
and causes the drop of the electrostatic binding energy? It is physically
possible or it's an artifact?
I wanted to attach the obtained graph and .pqr files to the e-mail but I had no luck with it as the attachments get rejected.
If you need to see the files can you please let me know how I can attach them?
The attachments are not bigger than few KB altogether.
I have been using a "focusing" approach to calculate the
electrostatic binding energy.
Any help will be greatly appreciated.
Thank you very very much in advance.
Davide Mercadante