[gmx-users] Protonation state of the ionisable residues

James Starlight jmsstarlight at gmail.com
Wed Feb 22 09:15:22 CET 2012

Dear Gromacs Users!

I'd like to change default protonation state of some specified Glu and Asp
residues im my protein.

By defaylt pdb2gmx -ignh create unprotonated state of the negatively
charged residues but I want to make 2 of such residues protonated to mimick
some intermollecular interactions.

How I could make such edition to my structure ? Is it possible to make such
changing AFTER pdb2gmx processing of my structure ( manually editiong GRO
or PDB file and TOPOLOGY)?


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