[gmx-users] HIS residue in Charmm27
s.neumann08 at gmail.com
Tue Feb 28 17:32:49 CET 2012
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?
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 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
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