AMBER Archive (2004)

Subject: Re: AMBER: free energy

From: Oliver Hucke (ohucke_at_u.washington.edu)
Date: Fri Jun 04 2004 - 14:19:25 CDT

I found the following article very informative wrt the different options
  when using MM-PBSA:

@Article{70857,
   author = {H. Gohlke and D. A. Case},
   title = {Converging free energy estimates: MM-PB(GB)SA studies on
the protein-protein complex Ras-Raf},
   journal = {J. Comput. Chem.},
   year = {2004},
   volume = {25},
   pages = {238-250},
}

Best,
Oliver

A. Hungie wrote:
> Dear All,
>
> I would like to compare free energy of two conformations of dimer, by
> taking into account water effect, also without water effect. What
> program should I use, MM-PBSA or GIBBS? If I should use MM-PBSA, should
> I use GB or PB method?
> Thank you very much in advance.
>
> Regards,
> Hungie
>
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-- 
_______________________________________________________________

Oliver Hucke, Dr.
                               Health Sciences Building - K418C
University of Washington      1959 NE Pacific St.
Dept. of Biochemistry         phone: (206) 685 7046
Box 357742                    fax  : (206) 685 7002
Seattle, WA 98195-7742        email: ohucke_at_u.washington.edu
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