Re: Parameters and topologies for aa at different protonation states

From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Fri Jan 23 2004 - 11:14:18 CST

Hello,

I can think of a couple of papers from the Daggett Group in Seattle
http://faculty.washington.edu/daggett

but others like Karplus and possibly vanGunsteren have published rationales
for low pH simulations.

If you look in the latest charmm27 topology files many of the protonation
states of pH sensitive residues are given as patches.

And finally, MD simulations of pH greatly oversimplify the problem and
_must_ be checked against experimental data. NMR titration data are
available for several popular proteins, but many proteins have little of
these data published.

Regards
Brian
On Fri, 23 Jan 2004, Bartosz Dobrzelecki wrote:

> 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).
>
> Regards,
> Bartek D.
>
> --
> Bartosz Dobrzelecki Theoretical Molecular Biophysics Group
> Nicolas Copernicus University, Torun, Poland
>
> PGP: http://www.phys.uni.torun.pl/~noplease/bdobrzelecki.pubkey
>

*****************************************************************
**Brian Bennion, Ph.D. **
**Computational and Systems Biology Division **
**Biology and Biotechnology Research Program **
**Lawrence Livermore National Laboratory **
**P.O. Box 808, L-448 bennion1_at_llnl.gov **
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