AMBER Archive (2009)
Subject: RE: [AMBER] Re: question_on_MMPBSA
From: Catein Catherine (askamber23_at_hotmail.com)
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?