RE: pka calculations and their use in simulations

From: Michel Espinoza-Fonseca (
Date: Mon Jul 11 2005 - 07:41:49 CDT

That's a very interesting question. According to what I know, those
"non-standard" residues are not included in the latest version of the
CHARMM ff. In the latest version you can find phosphorylated tyrosine,
threonine and serine, for example.
I guess you have to modify the existing topologies. I don't think it'll
be a problem. Good luck with the simulations!


-----Original Message-----
From: [] On
Behalf Of Richard Law
Sent: Sunday, July 10, 2005 6:12 PM
Subject: namd-l: pka calculations and their use in simulations

I wondered to what degree people used pka/pb calculations, such as
to set the protonation state of ionisable residues in simulations. Do
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
just delete the protons and accept a partial charge? Or as far as
concerned these residue states don't exist and that's ok?


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