On Fri, May 03, 2013, seçkin Boz wrote:
> You likely have zero Lennard-Jones parameters on the proton bound to
> oxygen.
>
> How can I add Lennard-Jones parameter for the proton?
You'll need to define a new atom type for hydrogen bound to the side chain
oxygen, and give it LJ parameters in the parm.dat (or frcmod) file.
Note that this tautomer was not considered in the Amber ff development: you'll
have to develop of force field that is convincing in terms of its properties.
...good luck...dac
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Received on Fri May 03 2013 - 12:30:03 PDT
