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
expect.
Mark
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