Re: [AMBER] Hybridization Question

From: Bill Ross <ross.cgl.ucsf.EDU>
Date: Sat, 3 Dec 2011 12:12:34 -0800

> > 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.

Another use for hybridization in leap is the 'add H' function in xleap.
I wonder if anyone has used that feature. In any case, I think you can
run ok without using addAtomTypes to define the atom.


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Received on Sat Dec 03 2011 - 12:30:02 PST
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