On Tue, Jul 12, 2016 at 12:21 AM, Thakur, Abhishek <axt651.miami.edu> wrote:
> Hi
> I was also confused that why igb =5 is used i stead of 2.
So I looked deeply into it and it says both are almost same model.
>
yes, they are based on the same model with a bit different in performance.
I think people used igb=5 because it's slightly better in term of
reproducing
PB solvation energy.
> I think they are working to develop new model for the system
> But as you can see in this reply they say igb=8 is more better
> http://archive.ambermd.org/201307/0765.html
>
> But no one clearly says the difference between all the models
>
>
Please check the corresponding citations for different GB models (you can
find them in manual). Don't just rely only on what people said on maillist.
When you use a model in your publication, you need to justify why you chose
that model (based on journal citation) rather saying
"I used that because someone in the maillist suggested to use".
After checking the doc and citations in the manual (
www.ambermd.org/doc12/Amber16.pdf, Section: The Generalized Born/Surface
Area Model),
if you are not clear about anything, please let us know.
cheers
Hai
> Sent using OWA for iPhone
> ________________________________
> From: Jason Swails <jason.swails.gmail.com>
> Sent: Monday, July 11, 2016 4:13:12 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] mmpbsa.py to calculate binding energy between protein
> and a ligand when there are two ligands combined with the protein.
>
> On Mon, Jul 11, 2016 at 10:55 PM, ZHU JH <jewelryono.outlook.com> wrote:
>
> > Dear Abhishek,
> >
> > When I consulted the amber manual,it says there is small
> > discrepancy between 'igb=2' and 'igb=5'.
> >
> > Another,I used sample input files of the amber manual for
> > reference.
> >
> > But,is there anything inappropriate to use'igb=5'?
> >
>
> ?igb = 2 and igb = 5 are not that different. If I recall correctly, igb =
> 5 is a more popular choice for MM/GBSA analyses because it has, in several
> studies, given results with better agreement to experiment.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
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Received on Mon Jul 11 2016 - 22:00:02 PDT
