AMBER: protonation states of small molecules

From: Lee, Matthew <>
Date: Fri, 15 Aug 2003 11:33:40 -0700

Fellow AMBER users--

        I am looking for a program that can, for a given pH, properly add
protons from amines and remove them from carboxylates and phosphates of
small molecules in an automated way and assign partial charges that will sum
up to the correct formal charge.

        Every 3D structure generator that I've used always protonates
carboxylates *and* deprotonates amines (to their neutral state), which is
not possible at any pH and thus not useful for accurate force field
calculations. Does anyone know a way around this, short of hand editing
each molecule?

--Matthew Lee

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Received on Fri Aug 15 2003 - 19:53:01 PDT
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