[gmx-users] pdb2gmx and protonated states of the residues

Brett brettliu123 at 163.com
Sun Apr 26 02:54:09 CEST 2015

Dear All,
By H++ and reduce we can have the input PDB for pdb2gmx have the initial corrected protonated states for some residues, for example, HIS, ARG, GLU and terminal residues. However biologically speaking with the change of the protein conformation, the protonated states of the above residues can be changed.
Will you please introduce to me how GROMACS deal with the possible protonation state change during the MD process?

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