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Tutorial-l Mailing List

From: Joao Ribeiro (jribeiro_at_ks.uiuc.edu)
Date: Tue Jan 21 2020 - 09:22:52 CST

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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 (http://www.ks.uiuc.edu/Research/vmd/plugins/qwikmd/#tblopt). Besides histidine, all residues are assigned with their default protonation state defined in the CHARMM forcefield.

Best,

João

From: <owner-tutorial-l_at_ks.uiuc.edu> on behalf of aabusaleh <aabusaleh_at_mun.ca>
Date: Monday, January 13, 2020 at 3:45 PM
To: <tutorial-l_at_ks.uiuc.edu>
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.

Thanks,

Aziz
 

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