i'm trying to measure the binding energy of a hydrophobic ligand to a
protein with a hydrophobic binding pocket in a aqueous medium.
cheers.
et
2012/3/21 Carlos Simmerling <carlos.simmerling.gmail.com>
> it all depends on what you are trying to accomplish.
>
> 2012/3/20 g t <sketchfoot.gmail.com>
>
> > Thanks for the information. :) could you suggest some particularly good
> > examples from the literature that stand out for you?
> >
> > best regards,
> > et
> >
> > 2012/3/20 Carlos Simmerling <carlos.simmerling.gmail.com>
> >
> > > this is an approximation, and various values have been used in the
> > > literature. there is no known "right" value to use, so as before I
> > suggest
> > > that you follow successful examples in the literature of things similar
> > to
> > > what you are doing.
> > >
> > > 2012/3/20 g t <sketchfoot.gmail.com>
> > >
> > > > Hi,
> > > >
> > > > I was having a look at the GBSA tutorials and had a query that
> someone
> > > > might help to resolve.
> > > >
> > > > Looking at the following page:
> > > >
> > > >
> > >
> >
> http://ringo.ams.sunysb.edu/index.php/2011_AMBER_Tutorial_with_Biotin_and_Streptavidin#MMGBSA
> > > >
> > > > It says that:
> > > >
> > > > ÄGnonpolar = SASA*0.00542 + 0.92
> > > >
> > > > I understand that the 0.00542 + 0.92 term is a correction term for
> > > MM-PBSA.
> > > > Where:
> > > > SURFTEN 0.00542
> > > > SURFOFF 0.92
> > > >
> > > > However, when running GBSA using the sander module (igb=1), I saw
> > someone
> > > > in the archives mention that the correct value for surften was
> 0.0072.
> > So
> > > > My question is whether surften becomes 0.0072 in the infile and
> becomes
> > > > ÄGnonpolar = SASA*0.0072 or if the previous values are correct.
> > > >
> > > > Thanks in advance,
> > > > ET
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Received on Wed Mar 21 2012 - 23:30:03 PDT
