On 2012-02-28 04:32:49PM +0000, Steven Neumann wrote: > Thank you Justin. According to pKalfa values at pH=7 HIS has q=+36e. In > this case is it better to treat as noncharged or positively charged (+1) as > we perform simulation at pH=7 ? How would you treat it?
CHARMM supports 2 neutral isomers (HSD/HSE, where the proton is on the delta or epsilon carbon of the ring) and the fully protonated version (HSP). Since the imidazole ring has a pKa of 6.1, if your pH is 7 and the sidechain is solvent accessible, most people will probably treat it as neutral. Anyway, if there is experimental data to suggest the protonation state of the sidechain, then you should use that information instead of guesstimating... > > Steven > > On Tue, Feb 28, 2012 at 4:02 PM, Justin A. Lemkul <[email protected]> wrote: > > > > > > > Steven Neumann wrote: > > > >> Dear Gmx Users, > >> Does anyone know why in Charmm27 ff under Gromacs the residue HIS is > >> taken as residue HSE from rtp file and written as NONcharged? > >> > >> > > > > pdb2gmx decides the protonation state to assign based on a hydrogen bond > > network search. This is true for all force fields. If you are unsatisfied > > with the chosen protonation, there are command line options to > > interactively change the protonation state of any titratable residues. > > > > -Justin > > > > -- > > ==============================**========== > > > > Justin A. Lemkul > > Ph.D. Candidate > > ICTAS Doctoral Scholar > > MILES-IGERT Trainee > > Department of Biochemistry > > Virginia Tech > > Blacksburg, VA > > jalemkul[at]vt.edu | (540) 231-9080 > > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > > > ==============================**========== > > -- > > gmx-users mailing list [email protected] > > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > > Please search the archive at http://www.gromacs.org/** > > Support/Mailing_Lists/Search<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 [email protected]. > > Can't post? Read > > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > > > -- > gmx-users mailing list [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- ================================================================== Peter C. Lai | University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street [email protected] | Birmingham AL 35294-4461 (205) 690-0808 | ================================================================== -- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
