From: Joao Ribeiro (
Date: Tue Jan 21 2020 - 09:22:52 CST

Hi Aziz,


Sorry for the delay in answering your email. QwikMD does not assign any particular protonation state when preparing the structure, except for histidine residues ( Besides histidine, all residues are assigned with their default protonation state defined in the CHARMM forcefield.






From: <> on behalf of aabusaleh <>
Date: Monday, January 13, 2020 at 3:45 PM
To: <>
Subject: tutorial-l: QwikMD protonation


Hello there,

Please, what is the approach that is used to protonate a protein of a pdb file when preparing a simulation through QwikMD.




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