[gmx-users] tyrosyl radical force field

[tarak karmakar]

Thanks Tsjerk,
In my system, I need to model one of the TYR side chains in radical
form. Now while doing that I need to get proper charges as you said.
According I have calculated the ESP charges in Gaussian for the TYR
radical [ unprotonated,neutral, terminals are capped with -NMe and
-COCH3] . Now can I take these charges to simulate the entire protein?

Can you please suggest me a proper protocol and some ways to get
proper charges (RESP e'm trying) to deal with this problem?
Thanks

On Wed, Oct 3, 2012 at 5:40 PM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:
> 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
> --
> 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



-- 
Tarak