ah, one more point about igb=8, 5, and 2.
igb=8 was extensively tested for proteins and nucleic acid simulations and
was shown to have significant improvement.
However, there is still limited testing igb8 with MMGBSA.
So far I only saw one recent publication comparing the performance of of
all GB models in AMBER (include igb8).
http://onlinelibrary.wiley.com/doi/10.1002/jcc.24011/full
(but their conclusion might not apply to your specific protein complex)
Hai
On Tue, Jul 12, 2016 at 12:36 AM, Hai Nguyen <nhai.qn.gmail.com> wrote:
> 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
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>>
>> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org_mailman_listinfo_amber&d=CwIGaQ&c=y2w-uYmhgFWijp_IQN0DhA&r=0Hah93XWYYBgmROOVcaccg&m=OFiXsryrUm1PdnXXyLSkn3l7yYM2K0Lz0PdwIUKdmxY&s=kA3rh9XCaS-8azymUeOuVE7AI88j7ntJkNYGU6lVAPY&e=
>> _______________________________________________
>> 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 Mon Jul 11 2016 - 22:00:02 PDT
