[gmx-users] Control Atoms for Hydroxide ?

Tsjerk Wassenaar tsjerkw at gmail.com
Tue Aug 18 09:05:31 CEST 2009


Well, who'd need control atoms? You'd just need to position it at a
certain distance along a random vector. If you're talking about it as
part of a water cluster or something, technically speaking it's not a
hydroxide anymore :) On another note, as I mentioned before, the
proton has an intrinsically ill-defined position. Please do understand
that we're not jsut trying to bully you here. At some point you have
to justify your model and a reviewer (which might be one of us :p) is
likely to raise the same issues we're doing here.



On Tue, Aug 18, 2009 at 2:47 AM, Mark Abraham<Mark.Abraham at anu.edu.au> wrote:
> 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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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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