Hi Geoff,
Don't get me wrong, I think that Babel is the best. But I am unable to use
Babel for various reasons (I am intending to implement a web-based docking
experiment, that is one of them). I've been using Babel to verify my
calculations. I'm so close to finishing, and I have everything nearly
completed except for the atom assignments and measurements.
So basically I would have to go through each smarts structure defined in
gaff.prm and see if there is a matching atom in the molecule?
Sorry, but my question remains as to how can element is assigned its atom
type based solely on bond connectivities.
Thanks,
- Eric
On Mon, Dec 19, 2011 at 8:44 PM, Geoff Hutchison
<ge...@geoffhutchison.net>wrote:
>
> 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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