[gmx-users] Re: His protonation

[Justin A. Lemkul]

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

You can manually set any protonation state you want with pdb2gmx -his.

-Justin

> 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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> 
> 
>       
> 
> 

-- 
========================================

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

========================================