At 13:09 17/09/2007, Sulev Sild wrote: >On Sep 16, 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: > >We also face this problem routinely while doing QSAR/QSPR modelling. Usually >we do it by workflows looking like the following:
Thanks, >- generate crude 3D geometry with MOLGEO (from Codessa Pro software package) >- perform conformational space analysis with macromodel Obviously it is more expensive if we need conformers. I am fudging that by only looking at molecules which are fairly rigid. It could actually be very valuable to store a few conformers for each new structure. For macroscopic properties such as NMR or IR we probably don't need anything less than 1% - that's a few kcal >- geometry optimisation with MOPAC This scales as ca N^3 or N^4 and it may be useful to do parts of large molecules separately. >Some steps there can be computationally quite demanding when large data >sets are dealt with. We have currently a Chemomentum project running to have >this kind of workflows running on a computational grids. We are pretty much >interested to have this kind of workflows performed with open source >software, to have this kind of workflows accessible for everyone. P. >Best wishes, >Sulev > >-- >Dr. Sulev Sild e-mail: [EMAIL PROTECTED] >Intitute of Chemistry, University of Tartu phone: (+372) 7375-254 >Jakobi 2, Tartu, Estonia, 51014 fax: (+372) 7375-264 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
