[gmx-users] tyrosyl radical force field

[Justin Lemkul]

On 10/3/12 7:49 AM, tarak karmakar wrote:
> 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 ?
>

That doesn't sound legitimate to me at all.  A radical species is electronically 
very different.

-Justin

> 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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>
>
>

-- 
========================================

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

========================================