> for example, C3 may mean [#6^3]. So how do I know what's mean of the extra > atoms; is there a list to explain them. I want to use them to match the > atom type in opls-aa forcefield.
I don't think the atom types defined by Open Babel are anywhere precise enough for OPLS-AA, which has specialized types for DNA/RNA and things like "aromatic C in 5-membered ring next to C and deprotonated N" http://towhee.sourceforge.net/forcefields/oplsaa.html In general, for force fields (e.g., MM3, MMFF94) you have to write your own atom typing procedure using Open Babel. This can be defined by SMARTS patterns, but in many cases, it's best to use both SMARTS typing and some coding as well. (Yes, many things can be defined by complicated SMARTS but that doesn't make it easy to understand.) -Geoff ------------------------------------------------------------------------------ Special Offer -- Download ArcSight Logger for FREE! Finally, a world-class log management solution at an even better price-free! And you'll get a free "Love Thy Logs" t-shirt when you download Logger. Secure your free ArcSight Logger TODAY! http://p.sf.net/sfu/arcsisghtdev2dev _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
