Hello,
MM/PBSA is a trajectory post-processing analysis. You should use a
trajectory that's already been generated for this analysis.
Good luck!
Jason
On Wed, Sep 22, 2010 at 12:30 AM, hirdesh kumar <hirdeshs8.gmail.com> wrote:
> 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
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Tue Sep 21 2010 - 22:00:04 PDT
