At 12:49 +0100 16/9/07, peter murray-rust wrote: >We have a real need to generate structures from 1-D connection tables and >there is no tried and trusted Blue Obelisk coordinate generator (e.g. we use >CDK for 2D coordinates and have run it over 200,000 structures). > >Here are the possibilities: >* look it up in crystaleye. This will work instantly for molecules which have >been done in the last 5-10 years. I suspect this will be very good for common >solvents, anions and cations, etc. Nick now has this under OpenBabel search >with SMARTS - try it out. >* use RDKIT. >* create a 2D picture, scale to 1.5 A bond length and optimize it in PM3. Not >as silly as it sounds. It will work well for flat molecules. It may also be >possible to distort the tetrahedral centres sufficiently to give the correct >chirality. >* hybrids. For anything with metal centres, and probably also complex rings, >use crystaleye moieties to start with. It may need some substitution or >addition. Then sprout some rough ligands. BUSTR (Sam Adams) did/does this. It >works, but needs reengineering. After that use PM3.
With a given connection table, the initial refinement is much best done using mechanics, which will NOT change the connection table. PM3 could well do this. We use the Ghemical system, but it currently implements only the Tripos FF. The UFF (universal force field) is a much better bet, but has not yet been implemented (the UFF IS documented, and open source). I realise none of this is off the shelf, but if Connection table => 3D UFF coordinates ==> PM6 ===> Gaussian could be made to work, it would I think be the most efficient. (thinking about it, the Gaussian program DOES implement UFF. so a Gaussian workflow of the type UFF --link1-- PM3 --link1-- 6-31G(d,p) might be viable. The --link1-- command by the way is how one daisy chains calculations together in Gaussian. -- Henry Rzepa. +44 (020) 7594 5774 (Voice); +44 (0870) 132 3747 (eFax); [EMAIL PROTECTED] (iChat) http://www.ch.ic.ac.uk/rzepa/ Dept. Chemistry, Imperial College London, SW7 2AZ, UK. (Voracious anti-spam filter in operation for received email. If expected reply not received, please phone/fax). ------------------------------------------------------------------------- This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2005. http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ _______________________________________________ Blueobelisk-discuss mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss
