different GB models give different treatment of solvent effects. none is
perfect, and none works best in all cases. it might be good to read the
articles about the GB models.
yes you can use gbsa=1 with any of the GB models in Amber. you will need to
specify a surface tension.
in general suggest that people try to find a peer-reviewed article in which
someone successfully did work similar to your own goals, and then use that
as a guide for how to proceed. if you can't find anything in the literature
where igb=2 was used for DNA, it might be a sign that it either isn't a good
model, or has not been tested well. you would need to treat it as an open
research problem.
On Thu, Apr 1, 2010 at 12:49 AM, maya maya <harish.maya83.gmail.com> wrote:
> Dear Amber !
>
> Thank you for the reply !
> Why one should not use the value igb=2 for the DNA , if they do so what
> will
> be the
> problem with the dynamics. Is it possible to use the flab gbsa=1 in both
> the
> cases (igb=1 & igb=2)
>
> I have a doubt what are the other flags that have to be taken care if one
> do
> the GB run for
> DNA
>
> regards
> maya
> _______________________________________________
> 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 Thu Apr 01 2010 - 05:30:05 PDT
