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 18:37:54 -0400

On Thu, Mar 21, 2013 at 11:52 AM, Miguel Ortiz Lombardía <
miguel.ortiz-lombardia.afmb.univ-mrs.fr> wrote:

>
> 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.
>

Ah, I guess I read too quickly. Well then in response to the Mg2+ question
from the OP, there is no prescription for dealing with explicit ions in PB
or GB solvents. You can try running the calculations including whatever
ions you want to include, but check the results carefully to make sure they
make sense.

I would also encourage searching the literature for researchers that tried
something similar to see how they approached the issue.

Good luck,
Jason

-- 
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu Mar 21 2013 - 16:00:03 PDT
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