FEP charge perturbation

From: Floris Buelens (floris_buelens_at_yahoo.com)
Date: Sun May 29 2005 - 17:50:28 CDT


I'm running FEP where I'm trying initially to
calculate the free energy difference between two bound
peptides differing in one position, one glutamate, one
For my thermodynamic cycle, I'm simulating the 11-mer
peptide in solution, but I'm unsure how to handle the
change in charge between the two forms. When going
from the glutamine-containing peptide (no net charge)
to the glutamate one (net -1), should I introduce a
compensatory cation?
I've found some discussion of this in the literature
but I'd appreciate comments if anyone has experience,
Thanks for your time,

Floris Buelens

Crystallography, Birkbeck College, London

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