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 <tsje...@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 <jalem...@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 <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 >>> >>> >>> >>> >> >> -- >> ======================================== >> >> 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 > > > > -- > 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@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 -- 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
