Re: [AMBER] Stability calculations from MMGB/PBSA

From: Andrea Spitaleri <andrea.spitaleri.iit.it>
Date: Thu, 12 Nov 2015 10:20:41 +0100

Hi,
have look to this very recent paper:

http://onlinelibrary.wiley.com/doi/10.1002/jcc.24235/abstract

HTH

and

On 12/11/2015 08:55, Rajeswari A. wrote:
> Thank you very much Carlos, David Case and Jason for your explanations and
> suggestions.
>
> Thanks once again.
> On Nov 11, 2015 7:03 PM, "Jason Swails" <jason.swails.gmail.com> wrote:
>
>> On Wed, Nov 11, 2015 at 3:54 AM, Rajeswari A. <rajeswari.biotech.gmail.com
>> wrote:
>>
>>> Dear all,
>>> I did protein and its mutants simulations. I wanted to calculate the
>>> ralative stability of mutant protein with respect to wild type protein.
>>>
>>> For that can i use MMGB/PBSA analysis specifying the protein as complex
>>> (although it is a single entity)?
>>>
>>> Using MMGBSA, the resultant difference between mutant and wildtype is
>> ~300
>>> Kcal/mol. Is the difference acceptable? Please suggest.
>>>
>> ‚ÄčAs Carlos and Dave pointed out, you usually want to do a delta-delta G (as
>> defined through some kind of thermodynamic cycle). The zero-point energy
>> for a force field is undefined (in fact, it's probably different for each
>> system), which means the only values that have any real, physical meaning
>> are energy differences *of the same system*.
>>
>> Subtracting the energy of a wild-type protein conformation from the energy
>> of a mutant protein conformation is a meaningless value. You can't compare
>> single-point energies, or conformational average energies between different
>> systems -- you can really only compare energy *differences* between
>> different systems (i.e., a delta-delta G).
>>
>> HTH,
>> Jason
>>
>> --
>> Jason M. Swails
>> BioMaPS,
>> Rutgers University
>> Postdoctoral Researcher
>> _______________________________________________
>> 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

-- 
Andrea Spitaleri PhD
Istituto Computational mOdelling of NanosCalE and bioPhysical sysTems -
CONCEPT LabItaliano di Tecnologia
Via Morego, 30 16163 Genova
cell: +39 3485188790
http://www.iit.it/en/d3-people/andrea-spitaleri.html
ORCID: http://orcid.org/0000-0003-3012-3557
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Nov 12 2015 - 01:30:05 PST
Custom Search