[gmx-users] Re: His protonation

[Rabab Toubar]

So is there a way we can make His neutral before running the simulations as in case of NAMD?
Rabab Toubar



--- On Wed, 6/16/10, Justin A. Lemkul <jalemkul at vt.edu> wrote:

> From: Justin A. Lemkul <jalemkul at vt.edu>
> Subject: [gmx-users] Re: His protonation
> To: "sagar barage" <sagarbarage at gmail.com>, "Gromacs Users' List" <gmx-users at gromacs.org>
> Date: Wednesday, June 16, 2010, 11:59 PM
> 
> Please keep all Gromacs-related correspondence on the
> gmx-users list.  I am not a private tutor.
> 
> sagar barage wrote:
> > Dear sir,
> >         
>    when i was done the MD of crystal
> structure the both nitrogen of immadazol ring of histidine
> is protonated
> > which are not protonated in crystal structure.
> 
> There are no protons in crystal structures.
> 
> >          all histidine in
> structure contain single protonation but some Histidine is
> double protonated at both nitrogen
> > why this happens in gromacs?
> > 
> 
> Please read the manual information (or pdb2gmx -h) about
> how pdb2gmx attempts to add hydrogens to the input
> structure.
> 
> -Justingm
> 
> > -- Sagar H. Barage
> > sagarbarage at gmail.com
> <mailto:sagarbarage at gmail.com>
> 
> -- ========================================
> 
> 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
> 
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