Re: FEP on charged residue mutation

From: Sebastian Stolzenberg (s.stolzenberg_at_gmail.com)
Date: Tue Nov 25 2008 - 19:48:21 CST

Dear All, Hi Jerome ;-),

I now have a different mutation: D2A.
The 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 I am afraid there will be
trouble arising from having both SOD and CL in solution (e.g. can
formation of NaCl cause any trouble?).

Thank you,
Sebastian

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