On Thu, Feb 20, 2014, Yew Mun Yip wrote:
> Hi, I ran antechamber on an organic molecule, and although there are no
> errors, the info message "Bond types are assigned for valence state 1 with
> penalty of 1" appeared. I just wish to ask what does this message mean?
The basic ideas of assigning bond types and valencies is discussed here:
%A J. Wang
%A W. Wang
%A P.A. Kollman
%A D.A. Case
%T Automatic atom type and bond type perception in molecular mechanical
calculations
%J J. Mol. Graphics Model.
%V 25
%P 247-260
%D 2006
But for the details of the integers that define valence states and penalties,
you will probably have to consult the source code. (Maybe someone on the list
knows of another source of information here.)
...dac
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Received on Thu Feb 20 2014 - 09:30:02 PST
