[gmx-users] protonation of histidines

[Tsjerk Wassenaar]

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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