[gmx-users] tyrosyl radical force field

[tarak karmakar]

Thanks Justin,
Actually if I would remove the proton from the tyrosine -OH and add
the corresponding charge of the Hydrogen to the phenolic oxygen to
keep the residue neutral then wouldn't it be convenient to think as if
it's a radical ?

On Wed, Oct 3, 2012 at 4:42 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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
>
> --
> ========================================
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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-- 
Tarak Karmakar
Molecular Simulation Lab.
Chemistry and Physics of Materials Unit
Jawaharlal Nehru Centre for Advanced Scientific Research
Jakkur P. O.
Bangalore - 560 064
Karnataka, INDIA
Ph. (lab) : +91-80-22082809