I think a better approach is to look at the atomic mass and match that to
what you see in the periodic table, but this runs the assumption that nobody
has changed these masses in the topology file.
I've written another email with the patched library file for you.
On Tue, Oct 4, 2011 at 1:25 PM, Peter Eastman <peastman.stanford.edu> wrote:
> > This has always been a real pain in things like QM/MM where one needs to
> know the atomic number but that
> > information does not reliably exist.
>
> Why not use the atomic numbers listed in the library file? I mean, each
> atom type does correspond to a unique element. You just need to know what
> that is, and that information is right there in the file (aside from the
> ones that say -1, which is just a bug).
>
No amber program outside of leap ever uses the library file, so this
approach won't help sqm.
All the best,
Jason
> > The routine I use in the QM/MM code is to take the Atom name (from the
> PDB file that gets processed into the prmtop
> > file) and then pull the first letter of this and then try to essentially
> figure out the element based on that and the mass.
>
> Yes, I've done the same thing on occasion, but as you say it's hard to do
> reliably. For example, CL means chlorine, not carbon, but CA means carbon,
> not calcium.
>
> Peter
>
>
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue Oct 04 2011 - 11:00:03 PDT
