On Thu, Nov 15, 2012 at 5:51 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 11/15/12 12:47 PM, Steven Neumann wrote: >> >> So what would you do to get those parameters asap? >> > > Get what parameters? The ones shown below (except Cu2+) have no citation > and no one has vouched for their authenticity. As such, the decision was > made to delete them to prevent anyone from blindly using them, hoping that > they are right. Given this information, it would be unwise to use them > unless, as I said, you know where they came from and believe them to be > suitable. > > -Justin
I found the source of the Fe(2+) parameters below from QM/MC simulations: http://www.sciencedirect.com/science/article/pii/S0009261407014388 Please, see table 1. I think it is a reasonable source for the usage Fe(2+) in aqueous solution with protein. Would you comment please? Steven > > >> On Thu, Nov 15, 2012 at 5:19 PM, Justin Lemkul <jalem...@vt.edu> wrote: >>> >>> >>> >>> On 11/15/12 12:18 PM, Steven Neumann wrote: >>>> >>>> >>>> Dear Gmx Users, >>>> >>>> Maybe someone before was simulating Fe(2+) in water and protein system >>>> using Charmm27 ff. I am looking for nonbonded parametrs. I found in >>>> OPLSAA: >>>> >>>> ; These ion atomtypes are NOT part of OPLS, but since they are >>>> ; needed for some proteins or tutorial Argon simulations we have added >>>> them. >>>> Cu2+ Cu2+ 29 63.54600 2.000 A 2.08470e-01 >>>> 4.76976e+00 >>>> Fe2+ Fe2+ 26 55.84700 2.000 A 2.59400e-01 >>>> 5.43920e-02 >>>> Zn2+ Zn2+ 30 65.37000 2.000 A 1.95200e-01 >>>> 9.78219e-01 >>>> Ar Ar 18 39.94800 0.000 A 3.41000e-01 >>>> 2.74580e-02 >>>> >>>> But not sure whether I can use them? >>>> >>> >>> These are undocumented parameters that are being removed for the next >>> release. Don't use them unless you can find where they came from and you >>> trust that source. >>> >>> -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 -- 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
