[gmx-users] Re: His protonation

Justin A. Lemkul jalemkul at vt.edu
Thu Jun 17 05:59:51 CEST 2010

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.


> -- 
> Sagar H. Barage
> sagarbarage at gmail.com <mailto:sagarbarage at gmail.com>


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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