[gmx-users] protonation of histidines

[Irem Altan]

Hi,

Thanks. Is there something I can read to get more information as to how this is done?

Best,
Irem

> On Jun 2, 2016, at 1:06 PM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:
> 
> Hi Irem,
> 
> pdb2gmx checks the hydrogen bonding network and decides which form of His
> fits best.
> 
> Cheers,
> 
> Tsjerk
> On Jun 2, 2016 17:20, "Irem Altan" <irem.altan at duke.edu> wrote:
> 
>> Hi,
>> 
>> When I process a .pdb structure using pdb2gmx, how does Gromacs add
>> hydrogens to the histidine residues? I see that in the processed structure,
>> some histidines have their NE2 atom protonated, while some have ND1
>> protonated. How does Gromacs decide which nitrogen to protonate?
>> 
>> Best,
>> Irem
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