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

Alex nedomacho at gmail.com
Sun Apr 26 03:37:24 CEST 2015

Aside from interacting with solvent-dissolved protons (if you add
them), the protonation states are permanent in GMX. All forcefields
used in these simulators are non-reactive (beyond vdw and

Unless you run your simulation in stages, where you
manually change protonation states, nothing chanes.


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

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