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
Received on Tue Mar 20 2012 - 16:30:04 PDT
