Re: [AMBER] mmpbsa calculations for a ternary protein/dna/ligand complex in presence of cocrystalized Mg ions

From: Jason Swails <jason.swails.gmail.com>
Date: Thu, 21 Mar 2013 11:36:19 -0400

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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Received on Thu Mar 21 2013 - 09:00:03 PDT