[apbs-users] Post-processing of MD trajectories

[Davide Mercadante]

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

[Baker, Nathan]

Hi Davide –

 

Are you using the same grid spacing and position for all calculations?  Variations in the grid setup could cause big changes in energy.

 

Thanks,

 

__________________________________________________
Nathan Baker
Pacific Northwest National Laboratory
Tel:  +1-509-375-3997
http://nabaker.me

[Davide Mercadante]

Dear Nathan, 

Thanks for your reply. Yes..all the parameters are exactly the same..

Thank you 

Davide

Davide Mercadante

PhD student - School of Chemical Sciences

The University of Auckland

New Zealand

[David Ramirez]

I Davide,

I would like to start to perform electrostatic calculation on Md trajectories for a ion channel using APBS. Can you help me in this process? and may be can you provide me the scrip that you use to plotted the electrostatic binding energy as a function of he simulation time.

Thanks for the help.

Regards