AMBER Archive (2005)

Subject: Re: AMBER: About Salt concentration

From: Varsha Goyal (vgusp_at_yahoo.ca)
Date: Fri Dec 16 2005 - 19:37:45 CST

Dear Jiri,

I am working on An Enzyme (protein) and trying to
stabilize it using MD. And i am not sure weather to
use any salt concentraiton or not??
Thanks,

--- Jiri Sponer <sponer_at_ncbr.chemi.muni.cz> wrote:

> Hi!
>
> It depends on what type of system do you have and
> what is your simulation goal.
>
> For nucleic acids, minimal neutralization salt is
> OK.
> We did few RNA systems and compared
> minimal Na+ with excess Mg2+ simulation, and did
> not see any really systematic cation effects, on
> typical time scales around 25 ns.
> Proteins might be different story.
>
> In general, Cl- could cause troubles, anions are
> polarisable
> species and less accurately described by pair
> additive
> force field than Na+.
>
> Others might disagree, but I prefer minimal salt and
> well tested Na+, for Nucl.Acids.
>
> Jiri
>
>
>
>
> [ Charset ISO-8859-1 unsupported, converting... ]
> > Dear Amber users,
> > I was wondering what happens of we use extra
> sodium
> > and chloride ions during Molecular Dynamics (
> meaning
> > use some particular salt concentration)?
> > Is it necessary? What difference does it make?
> >
> > Happy Holidays!!!!!!
> > Thanks a lot in Advance,
> > Varsha Gupta
> >
> >
> >
> >
> >
> >
> >
> >
>
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>
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> >
>
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