Hi Thomas,
As you have mentioned about the MM-PBSA calculation. So Does it mean that
the Liu has to run again the simulation including some more parameters for
MM-PBSA calculations in the starting script or he can do the MM-PBSA
analysis on the same previous output files. The question may be so weird but
as I am new to this term that's y i m asking.
Hirdesh
On Wed, Sep 22, 2010 at 9:48 AM, <steinbrt.rci.rutgers.edu> wrote:
> Hi,
>
> as Bill already wrote, the total potential energy of the protein is not
> what you want if you are comparing the stability of two solvated
> conformers. The total free energy change upon changing the conformation is
> much more useful here. This sounds like a perfect application for MM-PBSA,
> check out the examples in the MMPBSA directory of amber, one of them does
> exactly what you probably want.
>
> Kind Regards,
>
> Thomas
>
> On Tue, September 21, 2010 1:42 pm, Bill Ross wrote:
> >> I have completed two solvent explicit simulations for two possible
> >> conformations of my protein. In order to know which one is more stable,
> >> I need to compute the total potential energy form my protein
> >> without solvent.
> >
> > This might tell you which was more stable in vacuum. Is that useful?
> > E.g. the conformations may not even be attainable in vacuum.
> >
> > Bearing in mind that you may be on the wrong track, it is possible
> > to get the energy of the solute alone by extracting the coordinates
> > for just those atoms with ptraj, e.g. into pdb, then loadpdb and
> > saveamberparm to create a prmtop/inpcrd, and run a single-step
> > energy minimization.
> >
> > Bill
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> Dr. Thomas Steinbrecher
> BioMaps Institute
> Rutgers University
> 610 Taylor Rd.
> Piscataway, NJ 08854
>
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>
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Received on Tue Sep 21 2010 - 22:00:03 PDT
