Parameters and topologies for aa at different protonation states

From: Bartosz Dobrzelecki (
Date: Fri Jan 23 2004 - 06:45:26 CST

Dear colleges,

I would like to perform MD simulations of protein in various pH. Are
there any predefined parameters and topologies for charged amino acids
(ARG+ --> ARG0, LYS+ --> LYS0, GLU- --> GLU0, ect.)

Can you give me some references to papers dealing with this problem (MD
in acidic and basic environments).

Bartek D.

Bartosz Dobrzelecki         Theoretical Molecular Biophysics Group
                      Nicolas Copernicus University, Torun, Poland

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