pka calculations and their use in simulations

From: Richard Law (
Date: Sun Jul 10 2005 - 18:12:00 CDT

I wondered to what degree people used pka/pb calculations, such as delphi,
to set the protonation state of ionisable residues in simulations. Do you
always do this or never do it because you really don't think it's

Of course it's not so easy to set-up non-standard protonation states for
NAMD. In the Charmm forcefield there are easy to use patches to make
protonated aspartates and glutamates, several different histidines to
choose from, but no default neutral lysine or charged tyrosine. Has
everyone created their own topology for these two new residues? Or do you
just delete the protons and accept a partial charge? Or as far as you're
concerned these residue states don't exist and that's ok?


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