The advantages of GBSA is that is faster and the setup is much easier.
However, as Carlos authoritatively mentioned, the results are highly
dependent on the used parameterization set, so the performances of the
available GB models (HCT, OBC, Neck2) should be evaluated against a
"test set" for your specific question.
Best,
Alessandro
Il 24/10/2017 21:46, sangita kachhap ha scritto:
> Thanks Alessandro. In addition to speed, is there any advantage to consider
> GBSA over PBSA?
>
>
>
>
>
> On Tue, Oct 24, 2017 at 8:36 PM, Alessandro Contini <
> alessandro.contini.unimi.it> wrote:
>
>> Hi Sangita,
>> I'm one of those that reported somehow better results from GBSA than for
>> PBSA, but this is contectual to the field of application. In our case
>> (http://pubs.acs.org/doi/abs/10.1021/ct400045d or
>> http://pubs.acs.org/doi/abs/10.1021/acs.jcim.6b00196) we were looking
>> for a protocol to quickly score several complexes, so speed was quite a
>> concern. Indeed, we postprocessed quite short MD trajectories (~4 ns)
>> and, being GB more approximated than PB, it also seemed to be less
>> sensitive to the MD simulation lenght. Using PB in such approximate
>> calculations would have been like using a precision scope on a shotgun
>> (it would hardly improve the probability of hitting the target).
>>
>> All the best,
>>
>> Alessandro
>>
>> Il 24/10/2017 16:00, sangita kachhap ha scritto:
>>> 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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>>>>>
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>> --
>> Alessandro Contini, PhD
>> Dipartimento di Scienze Farmaceutiche
>> Sezione di Chimica Generale e Organica "A. Marchesini"
>> Via Venezian, 21 20133 Milano
>> tel. +390250314480
>> e-mail alessandro.contini.unimi.it
>> skype alessandrocontini
>>
>> http://www.scopus.com/authid/detail.url?authorId=7003441091
>> http://orcid.org/0000-0002-4394-8956
>> http://www.researcherid.com/rid/F-5064-2012
>>
>>
>>
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--
Alessandro Contini, PhD
Dipartimento di Scienze Farmaceutiche
Sezione di Chimica Generale e Organica "A. Marchesini"
Via Venezian, 21 20133 Milano
tel. +390250314480
e-mail alessandro.contini.unimi.it
skype alessandrocontini
http://www.scopus.com/authid/detail.url?authorId=7003441091
http://orcid.org/0000-0002-4394-8956
http://www.researcherid.com/rid/F-5064-2012
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Received on Wed Oct 25 2017 - 00:30:02 PDT
