Hi again
Sorry if I disturb you, but i want to start in a good way my AMBER
calculations.
I have a last question.
I want to compare calculated interaction energies (ligand-protein) in the
surface of a protein
with biological data.
The ph of the media for the receptor, in the kit of our biological assays is
7.4 (biological 6.4-7.5)
so ... Is this the pH that I should use in my calculations?
My other concern is choose a good method to do it
As far as i know, i could use FEP. but i am not sure if it is the best
election
I have other alternatives in mind ... NAMD or ONIOM (gaussian)
Sorry again ... and thank you anyway for your help
I think that I am really close to start with AMBER
Fernando
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Received on Thu Apr 14 2011 - 07:00:03 PDT
