[gmx-users] Is there a way to add protons to all the residues in a pdb file that was run with the protons missing?

[Arthur Roberts]

Hi, all,

This is probably an obvious question.  I did a simulation with an  
ff53a6 force field, which lacks protons on aliphatic side chains.  I  
have pdb coordinates for each time.  Is there a way to add protons to  
the aliphatic side chains.  Your input is appreciated.

Sincerely,
Art Roberts