Re: pka calculations and their use in simulations

From: Darren Anderson (
Date: Mon Jul 11 2005 - 08:49:20 CDT

For that matter, different protonation states for things like ATP and
other triphosphates are another serious problem; we've created a couple
different versions for ATP/CTP/GTP/TTP/UTP (and will release them to the
user community once we're happy with them), but I'm always surprised so
few non-physiological charge states have been paramaterized.



> 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
> necessary?
> 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?
> Rich.

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