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.
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
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 - 21:30:02 PDT
