On Wed, Oct 7, 2015 at 11:06 PM, David A Case <david.case.rutgers.edu>
wrote:
> On Wed, Oct 07, 2015, Jonathan Sheehan wrote:
> >
> > The .prep and .frcmod files both refer to the atomtype "O3". They
> > don't specify its atomic number, and I don't see a way to add that,
> > using the current .frcmod format.
>
> Atomic numbers need to be added by an "addAtomTypes" command to LEaP.
> (This actually establishes the element name, but that is converted to
> atomic
> number internally in the code.) This is generally done in leaprc files,
> but
> it can also be entered in any LEaP input file:
>
> AddAtomTypes {
> { "O3" "O" "sp2" }
> }
>
> It is arguably a bug-let that you can't put such information into the
> frcmod file itself, since that would collect all relevant information
> about a new atom type (like O3) into a single file. But the code that
> reads the frcmod file is pretty primitive, and I'm not sure how easy it
> would be to allow it to recognize and process AddAtomType commands.
>
​Unless I'm mistaken, James Maier added the ability to read hybridization
information from the frcmod file. It might not be hard to extend that to
reading atomic numbers as well.
All the best,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Oct 08 2015 - 05:00:04 PDT
