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
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Mar 21 2012 - 04:30:02 PDT
