[gmx-users] Protonation state of aminoacids from pdb and pdb2gmx

[Justin Lemkul]

On 4/6/20 8:10 AM, Javier Luque Di Salvo wrote:
> Dear Gromacs users,
>
> I'm aware that there might be plenty of discussions on this matter, anyway
> I would like to get your advice. Which is the proper way to know the
> protonation state that is generated with pdb2gmx? I have downloaded a pdb
> file from the Protein Data Bank. The structure has no hydrogens, these are
> added by pdb2mx.
>
> Is this information usually available on the original pdb (like residue
> names) or in the generated topology? I would like to know where to search.

pdb2gmx assigns protonation states at neutral pH assuming canonical pKa 
values for all residues. That assumption is usually good, but obviously 
is not always correct, in which case you need to manually assign the 
protonation states using command-line options.

-Justin

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Justin A. Lemkul, Ph.D.
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