Hi Jason,
Well, I did not answer to the Mg2+ question ;-)
As for NAB not dealing with non-linear PB, I may be wrong, it may be
incompatible with some other option... I carried out many tests and
somehow this is what I remember. But I cannot track down now why I think
NAB does not deal with non-linear PB, sorry.
Cheers,
Miguel
Le 21/03/13 16:36, Jason Swails a écrit :
> Did you get Miguel's email to your last thread? He answered your question there.
>
> I was not aware that the nonlinear option did not work in NAB (the pbsa code used in both nab and sander is the same). But using sander should be fine.
>
> Good luck,
> Jason
>
> --
> Jason M. Swails
> Quantum Theory Project
> University of Florida
> Ph.D. Candidate
> 352-392-4032
>
> On Mar 21, 2013, at 11:26 AM, Giulia <giulia.palermo.iit.it> wrote:
>
>> Dear all,
>>
>> I am running some MMPBSA post-processing calculations on a ternary system composed by PROTEIN, DNA and a LIGAND intercalating the dna.
>> I am considering the protein/dna complex as the RECEPTOR, whereas the intercalating ligand is (effectively) the LIGAND.
>> A total of 60 frames is processed on 12 processors (5 frames per processor).
>> I am using the non-linearized PB equation for deriving the binding free energies in the thermodynamic cycle.
>>
>> In my system, there are six cocrystallized Mg2+ ions that are crucial for anchoring the DNA to the protein and for attaining the catalytic mechanism. Therefore, these Mg2+ can not be deleted.
>>
>> I wonder if there is any particular procedure for the treatment of the Mg2+ ions in MMPBSA calculations, using the non-linearized PB equation.
>>
>> Do you have any suggestion??
>>
>> thank you very much
>>
>> Giulia
>>
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--
Miguel Ortiz Lombardía
Architecture et Fonction des Macromolécules Biologiques (UMR7257)
CNRS, Aix-Marseille Université
Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France
Tel: +33(0) 491 82 55 93
Fax: +33(0) 491 26 67 20
mailto:miguel.ortiz-lombardia.afmb.univ-mrs.fr
http://www.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia
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Received on Thu Mar 21 2013 - 09:00:03 PDT
