[gmx-users] tyrosyl radical force field

Justin Lemkul jalemkul at vt.edu
Wed Oct 3 13:12:47 CEST 2012

On 10/3/12 6:00 AM, tarak karmakar wrote:
> Dear All,
> Is it possible to deal a protein with tyrosyl radical in Molecular
> Dynamics Simulation ?? If possible can you please provide me the
> reference or literature where I can find the force field parameters
> for tyrosyl radical ?

Molecular mechanics force fields do not deal explicitly with electrons, so don't 
expect anything particularly interesting to happen with a so-called radical 
tyrosine unless you're using QM methods.  You could perhaps parameterize a 
deprotonated tyrosine residue that, as input to QM software, has the number of 
electrons in the radical species.  You may then have to come up with new atom 
types depending upon whether or not the LJ parameters (especially for the 
phenolic O) are satisfactory.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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