Dear Dr. Oliver Hucke;
Thank you very much for your information.
The article is a good help to understand the examples of mm_pbsa, the
protein-protein complex Ras-Raf.
1) it isn't an usual complex of ligand and receptor but a protein-protein
complex .
2) how long does it take to get proper snap shots from single or separate
trajectories?
3) the meaning of solvent effects, etc.
Sincerely Yours.
Kazuo Koyano
----- Original Message -----
From: "Oliver Hucke" <ohucke.u.washington.edu>
To: <amber.scripps.edu>
Sent: Saturday, June 05, 2004 4:19 AM
Subject: Re: AMBER: free energy
> 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.u.washington.edu
> _______________________________________________________________
>
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Received on Mon Jun 28 2004 - 09:53:00 PDT
