On Dec 19, 2011, at 7:48 PM, Eric Jang wrote:
> 1. Is the assignment of atom types somehow based on the SMARTS string of a
> molecule? It would make sense that each atom has some SMARTS string property
> that is compared to the gaff.prm file.
SMARTS is essentially a programming language. So atoms might match zillions of
possible SMARTS. I'd think of it the other way around -- the gaff.prm defines
some SMARTS patterns which define atom types in the force field. Some of those
may match a particular molecule. Other force fields have other patterns and
atom typing rules.
...
> 3. How do I assign the GAFF atom types given what I know?
My suggestion is to use Open Babel. Take a look, for example at the Tinker
format, which provides element, X, Y, Z coordinate, and atom type. If you
replace "MMFF94" with "GAFF" it would give you an example at assigning GAFF
atom types for anything Open Babel reads. At that point, it's easier to write a
file (e.g., simple CML) run it through babel, and read the resulting Tinker
file.
That's the whole point -- in many ways, cheminformatics tasks can often be
handled directly by babel.
Hope that helps,
-Geoff
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