Hi
I am a new user of HADDOCK and am trying to figure out how you calculate the energy terms of BSA and desolvations. I can want the eq in the articles I read. all I can find is “E desolv is an empirical desolvation term and BSA is the buried surface area upon complex formation in Å2”.
Where can I find the function itself?
Thank you very much
michael
Slide from a presentation explaining it (and giving the references):
For the desolation, we are using the parameters from Fernandez-Recio et al JMB 335, 843 (2004)
Thank you so much!!
one last question, how is the Eair calculated? is it only from restraints violation?
if so, I don’t understand since I when I ran docking all my restraints were filled but the was still some penalty energy.
Thanks again,
michael
Yes the Eair is from the distance restraint energy. The upper limit is 2A.
Here is a one slide explanation:
Thank you
I’m not sure I understood. The Eair is the ENoe? Where does the effctive distance come in? and what do you mean by an upper limit of 2? U mean the have to be within 2 from each other?
And last, if I only put in unambiguous restraints and they were filled, how can there be restraints violation?
Sorry for all the questions
And thank you very much!
Eair is the same as Enoe
I’m not sure I understood. The Eair is the ENoe? Where does the effctive distance come in? and what do you mean by an upper limit of 2? U mean the have to be within 2 from each other?
Calculated over all possible distance combinations defined in the atom selections.
Did you upload your own restraints? And did not define any active/passive via the server interface?
In that case the restraint energy should only come from your restraints (unless the server detected a chain break and added some distance restraints to keep the different parts together.
And again, how do you know all your restraints are satisfied? Even very small violations will lead to some energy.