Re: FEP on charged residue mutation

From: Sebastian Stolzenberg (
Date: Tue Nov 25 2008 - 19:30:08 CST

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
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,

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