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

[Justin Lemkul]

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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Justin A. Lemkul, Ph.D.
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