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?
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> >
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