Re: FEP on charged residue mutation

From: Jerome Henin (jhenin_at_cmm.chem.upenn.edu)
Date: Tue Nov 25 2008 - 20:26:41 CST

Hi Sebastian,
There is no particular problem with mutating a chloride in an
environment containing sodium. You'd have to pay close attention to
convergence of the FEP average, but only if what you were interested
in was the precise value of deltaG :-)
Jerome

On Tue, Nov 25, 2008 at 8:30 PM, Sebastian Stolzenberg
<s.stolzenberg_at_gmail.com> wrote:
> Dear All, Hi Jerome ;-),
>
> I now have a different mutation: D2A.
> My initial structure has only SOD counter-ions to balance the system's net
> charge to zero.
>
> Within the FEP frame, I need to either
> a) fep-gradually replace a SOD by a water
> or
> b) fep-gradually replace a water by a CL
>
> to balance out the non-zero net charges arising from the mutation.
>
> More convenient for me is choice b), but could there be any trouble arising
> from having both SOD and CL in solutions (e.g. can formations of NaCl cause
> any significant trouble?).
>
> Thank you,
> Sebastian
>

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