Dear All,
I could like to calculate the interaction energy between domain 1 and 2 of a protein with four connected domains. I could like to know if we can still use MM/GBSA to do this calculation? If yes, I have the following questions,
Can I just assume both end of the domains I and II are cleaved, when I define prmtop files for domain 1 and 2 and defined as ligand and receptor, respectively in MM/GBSA calculations?
The mdcrd files I got from the MD simulations contain four domains, would it be a problem?
Best regards,
CAt
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Received on Wed Sep 02 2009 - 23:05:33 PDT
