On 2013-04-30 10:43, David van der Spoel wrote: > On 2013-04-26 21:22, Geoffrey Hutchison wrote: >>> I assume it works like this that OB determines the atom type to be HO (H >>> bound to O). >> >> No, no. This file is like a big translation dictionary. It says "if an atom >> type comes in from a PCModel file with atom type X," that's equivalent to .. >> well, everything on that row. Obviously, this need not be a one to one >> mapping. HO is a particularly good example, since I think PCModel has the >> "MMX" force field and separates between different types of HO hydrogens -- >> sorry I can't find the MMX atom type list right now. >> >> So we could, in principal, have the internal atom types as a superset of all >> atom types, but I think this is a bit crazy. >> >> If you want the internal atom typing rules, see data/atomtyp.txt >> (particularly EXTTYP). >> >> Hope that helps, >> -Geoff >> > Thanks for pointing that out. This means in practice that OB can not > distinguish between all those atomtypes that are used in random > packages, right? > > It would still be useful to have a textual description of each OB atom > type, what information there is in atomtyp.txt is not very descriptive. > > Let me just expand on why I am interested in this:
we are busy developing a new force field, and would like to use the OB types as the basis, to be translated to new force field atom types, which would need to be a subset of these types. On a side note, it seems that a number of Nitrogen atom types have atomnumber 6 (or maybe Rar and R are carbons anyway?) Rar 6 0 62 1 C C 3 C 2 R.ar 33 C C 2 1 C.0 26 1 R 6 0 62 1 C C 3 C 2 R. 33 C C 2 1 C.0 26 1 Nr 6 0 62 8 C C 3 C 2 Nr. 33 C C 2 1 C.0 26 8 -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.se http://folding.bmc.uu.se ------------------------------------------------------------------------------ Introducing AppDynamics Lite, a free troubleshooting tool for Java/.NET Get 100% visibility into your production application - at no cost. Code-level diagnostics for performance bottlenecks with <2% overhead Download for free and get started troubleshooting in minutes. http://p.sf.net/sfu/appdyn_d2d_ap1 _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
