AMBER Archive (2009)

Subject: RE: [AMBER] Re: question_on_MMPBSA

From: Catein Catherine (askamber23_at_hotmail.com)
Date: Thu Aug 27 2009 - 00:55:59 CDT

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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