Re: [gmx-users] tyrosyl radical force field
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 listgmx-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
Re: [gmx-users] tyrosyl radical force field
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 listgmx-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 listgmx-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
Re: [gmx-users] tyrosyl radical force field
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 listgmx-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 listgmx-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
Re: [gmx-users] tyrosyl radical force field
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 listgmx-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 listgmx-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 listgmx-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
Re: [gmx-users] tyrosyl radical force field
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 listgmx-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 listgmx-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 listgmx-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 listgmx-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
