The Molecular Graphics Laboratory Forum

Dear list I'm a very newbie user of the docking programs.
Actually I'm trying to dock some molecules (benzene poli Cl substituted), into my receptors. All the solutions found by autodock are with no hbond but with a big decrease in the binding energy(-8.79) for the obtained complexes.
In your opinion are these solutions reasonables?
thank you very much for any opinion you can give to me

Hi Guido,

from your post it's not clear what's the problem.
In particular, it's not clear why the lack of hydrogen bonds is a problem (chloro-benzene shouldn't form them, right?) and to which you refer to estimate the energy decrease.

Please, clarify those points so we can try to help you.


Stefano

hi guido,

can you describe it further? how you said it is very vague. the big energy decrease may be caused by something you failed to mention.

I would really like to help, but like the others have said I'm not real clear on the question/problem. please clairify.

I'm sorry for the late reply.
I'll try to further explain my perplexities.
I'm trying to dock some Polychlorinated biphenyl molecules into the binding site of one nuclear receptor (Era). The receptor is created following the tutorial (addyng polar hydrogen, checking the charges so on and so for...)
I observed for all my molecules a similar decrease in binding energy (-7;-8) even if the substitutions in each molecule are on different aromatic carbons.
First question: according to your experience could this small difference be representative of a different biological activity?
Second question:
As you say these molecules cannot make hydrogen bonds. Therefore could be possible that the scoring function of vina is not as sensitive to recognize the differences in binding energy due only to the hydrophobic interactions?
Thank you very much
Guido