[gmx-users] changing protonation state of a residue during a simulation

Payman Pirzadeh ppirzade at ucalgary.ca
Thu May 16 01:14:38 CEST 2013

I am simulating a protein using side chain pKa values estimated from
PROPKA based on crystal structure of the protein. I re-estimated the pKa
of side chains after running 10 independent replica of 50ns (500ns in
total) of NPT simulations. It turned out that the average pKa of a
surface Glu was overestimated in the crystal structure (protonated), and
needs to be reconsidered (not protonated). I was wondering how I can
re-assign the protonation state of this single residue without going
through pdb2gmx (or may be I have to) to keep the current conformation
of the protein and currently equilibrated solvent molecules? Is there a
way to continue the current simulations I have and only change the
charge of this single surface Glu?
Thanks for your help.


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