Thanks for the reply Carlos. I will check these article.
On Tue, Oct 24, 2017 at 3:51 PM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> I think it's a good idea to do what you mentioned, look at articles that
> have tested the methods for performance on problems similar to yours.
> However, as a GB developer, my opinion is that GB is really very
> approximate and I only use it where speed is most important (such as in
> MD). In postprocessing, speed is probably much less important than
> accuracy, and in those cases I opt for PB over GB. Also keep in mind that
> there are many different GB models, and their performance might differ for
> your problem. For example, when we developed the GBneck2 model in Amber
> (igb=8), we optimized for proteins and nucleic acids, but NOT for small
> molecule ligands. I would not expect it to perform as well as PB since no
> data of that type were included in the training or the testing.
> carlos
>
> On Tue, Oct 24, 2017 at 9:47 AM, sangita kachhap <nckachap.cyf-kr.edu.pl>
> wrote:
>
> > Dear Amber developer
> > I have to compare the binding free energies of different small molecule
> > ligands with a protein. According to some of the research article GBSA
> > method is good in ranking the free energies of ligands than PBSA. So
> which
> > method is actually more reliable for comparing the binding free energies
> of
> > ligands.
> >
> > If difference of binding free energies of two ligands is 5-6 kca/mole.
> Are
> > these methods able discriminate the such energy difference?
> >
> > Thanks
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Received on Tue Oct 24 2017 - 07:30:03 PDT
