On Fri, Dec 02, 2011, Sasha Perkins wrote:
>
> I was wondering if there is any way to add an atom type with an sp3d2
> hybridization using the addAtomTypes command in tleap. I have created and
> loaded a frcmod file for my molecule. Additionally, I will be using the
> gaff force field. I tried addAtomTypes { {"p7" "P" "sp3d2" } } and I get
> the following message: atom type p7 - unknown hybridization sp3d2.
Amber doesn't really use hybridizations for much of anything, and the force
fields ignore them completely. The only place they are used (that I know
of) is in the "relax selection" option of xleap, which can do an initial
optimization without knowing the force field. Adding a new type of
hybridization there would be a programming task.
...good luck...dac
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Received on Sat Dec 03 2011 - 07:00:02 PST
