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

Justin Lemkul jalemkul at vt.edu
Mon Sep 24 11:51:18 CEST 2012

On 9/24/12 3:33 AM, Albert wrote:
> Dear:
>   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 purpose?

Calculate pKa values, then assign protonation states with the appropriate flags 
to pdb2gmx (see pdb2gmx -h for all available options).  Renaming residues is 



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list