From: Alessandro Contini <>
Date: Tue, 24 Oct 2017 17:06:50 +0200

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
( or 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,


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 <
>> 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 <>
>> 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
>>> _______________________________________________
>>> AMBER mailing list
>> _______________________________________________
>> AMBER mailing list
> _______________________________________________
> AMBER mailing list

Alessandro Contini, PhD
Dipartimento di Scienze Farmaceutiche
Sezione di Chimica Generale e Organica "A. Marchesini"
Via Venezian, 21 20133 Milano
tel. +390250314480
skype alessandrocontini
AMBER mailing list
Received on Tue Oct 24 2017 - 08:30:03 PDT
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