AMBER Archive (2009)

Subject: Re: [AMBER] Re: question_on_MMPBSA

From: jackie (youban.xm_at_gmail.com)
Date: Thu Aug 27 2009 - 10:41:28 CDT

Dear Catein Catherine:

you can try to calculate all the residues contribution to the total binding
free energy with the item of decompostion 1 or 2, then. you can collect the
regions or domains where you are interesting in to sum them manually.
good luck

zhenhui jackie

2009/8/27 Catein Catherine <askamber23_at_hotmail.com>

>
> 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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