At 13:09 16/09/2007, Rzepa, Henry wrote:
>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. Excellent. In practice with PM5 we found that MOPAC rarely trashed organic structures and often refined them well. The main problems will be tetrahedral centres and cyclohexane rings (which often end up as twist-boats). I would filer these post hoc, shake them and recompute. P. >-- > >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). Peter Murray-Rust Unilever Centre for Molecular Sciences Informatics University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK +44-1223-763069 ------------------------------------------------------------------------- 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
