[gmx-users] how to assign protonation sate at pH-8?

Albert mailmd2011 at gmail.com
Mon Sep 24 09:33:25 CEST 2012


  My protein is only stable at pH-8.0 and I am wondering how can we 
assign the residues' protonation state for pH 8.0? Shall we calculate 
first by other pKA prediction software, then make modification to the 
residues' name according to the results manually in the PDB files so 
that gromacs can assign the correct protonation state for related 
residues? Or there are some internal methods in Gromacs for such kind of 

thank you very much

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