[gmx-users] HIS residue in Charmm27

[Peter C. Lai]

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 <jalemkul at vt.edu> 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>
> >
> > ==============================**==========
> > --
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Peter C. Lai			| University of Alabama-Birmingham
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