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

[Javier Luque Di Salvo]

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.

Javier

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*Javier Luque Di Salvo*

Dipartamento di Ingegneria Chimica

Universitá Degli Studi di Palerm*o*