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 <jalem...@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@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-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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 -- gmx-users mailing list gmx-users@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-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
