AMBER Archive (2004)

Subject: Re: AMBER: free energy

From: Carlos Simmerling (carlos_at_ilion.bio.sunysb.edu)
Date: Mon Jun 28 2004 - 08:06:43 CDT

If you are doing MM-PBSA on Ras/Raf, the you should probably read
this article if you haven't already:

%A H. Gohlke
%A D.A. Case
%T Converging Free Energy Estimates: MM-PB(GB)SA Studies on the
Protein-Protein Complex Ras-Raf
%J J. Comput. Chem.
%V 25
%P 238-250

----- Original Message -----
From: "Kazuo Koyano" <koyano_at_fsis.iis.u-tokyo.ac.jp>
To: <amber_at_scripps.edu>
Sent: Monday, June 28, 2004 4:45 AM
Subject: Re: AMBER: free energy

> 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_at_u.washington.edu>
> To: <amber_at_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
> > >
> > > _________________________________________________________________
> > > STOP MORE SPAM with the new MSN 8 and get 2 months FREE*
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> >
> -----------------------------------------------------------------------
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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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