[gmx-users] -ignh command removes protonation site of interest

[Quyen Vu]

Or another way to keep the protonated state of residue is using -asp, -glu,
-his ... and then you can manually assign the protonation state

On Tue, Apr 16, 2019 at 1:06 AM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 4/15/19 6:30 PM, Neena Susan Eappen wrote:
> > Hello gromacs users,
> >
> > I started with a peptide where protonation site was on a carbonyl
> oxygen. However, using -ignh command in pdb2gmx, I lose that proton from
> there. Any insights on how to move forward?
>
> If you want another protonation state, then you need to make sure the
> residue is named as expected by the force field (e.g. ASPP for
> protonated aspartate, not ASP, etc).
>
> -Justin
>
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