On Jul 27, 2011, at 4:19 PM, David Cantu <cantudav.amber.gmail.com>
> I am manually assigning Gaff atom types.
>
> Would the oxygen in a deprotonotaed hydroxyl group (RO- instead of ROH) be
> Gaff atom type (o) or (oh)?
The "general" Amber force field is not (yet) general enough: the calibration/optimization never considered deprotonated alcohols. If it makes an important difference, one would probably need to define and parameterize new atom types.
...dac
>
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Received on Wed Jul 27 2011 - 16:30:02 PDT
