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
Received on Tue Mar 20 2012 - 11:00:02 PDT
