[gmx-users] Control Atoms for Hydroxide ?

Mark Abraham Mark.Abraham at anu.edu.au
Tue Aug 18 02:47:53 CEST 2009

Marc Charendoff wrote:
> Sorry for bringing up the hydroxide ion question again, but are there any hints as to how to place a single hydrogen on the oxygen atom? Can I somehow assign control atoms outside the hydroxide anion as a means of reference for the required  ffG43a1.hdb modification? Looks like both methods to attach single protons need some kind of reference (control atoms).  Thanks much,

Was this ion parameterized for this (any?) forcefield? It seems quite 
unlikely that a classical hydrogen-oxygen bonded pair with net negative 
charge used with a classical water model could adequately model the kind 
of labile hydrogen-bonding activity that these species undergo.

Accordingly, it's not much of a surprise that GROMACS has no .hdb 
mechanism for generating a hydroxide hydrogen. The only reasonable way 
of generating coordinates would be by finding the most favourable 
electrostatic position, which would require modification of genion, I 


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