[gmx-users] tyrosyl radical force field

[Tsjerk Wassenaar]

It's a radical approach, for certain! But do mind that the tyrosyl
side chain is a conjugated system, so the charge goes all over the
place, and you have to do (proper) QM calculations to see where it
ends up. Radical approaches are not suitable for radical parameters :p

Tsjerk

On Wed, Oct 3, 2012 at 2:01 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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
>>>
>>> ========================================
>>> --
>>> gmx-users mailing list    gmx-users at gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> * Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>> * Please don't post (un)subscribe requests to the list. Use the www
>>> interface or send it to gmx-users-request at gromacs.org.
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>>
>>
>>
>
> --
> ========================================
>
> 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
>
> ========================================
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists



-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Biocomputing Group
Department of Biological Sciences
2500 University Drive NW
Calgary, AB T2N 1N4
Canada