Re: [Avogadro-Discuss] (no subject)
Dear Mike, if you do not believe UFF and MMFF optimizations, you can use some of the extensions in Avogadro and do some QM GeoOpt calculations. Avogadro has extensions to many QM programs, NWchem, and Gamess are free. GeoOpt in NWchem with DFT B3LYP should give you good geometry if you have less than 50 atoms. :-) On 2016-03-02 21:54, Michael Morgan wrote: > Dear Avogadro users, > > If I build a molecule from "File" > "Import" > "Fetch by chemical name…", how exactly is the molecule built? How much can I trust > the bond angle or bond length building this way? > > Thank you very much. > > Best regards, > > Michael -- **address file*** Željko Svedružić Ph.D. zsved...@biol.pmf.hr web: https://profiles.google.com/106720515809875304148#106720515809875304148/about ** -- Site24x7 APM Insight: Get Deep Visibility into Application Performance APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month Monitor end-to-end web transactions and take corrective actions now Troubleshoot faster and improve end-user experience. Signup Now! http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140___ Avogadro-Discuss mailing list Avogadro-Discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/avogadro-discuss
Re: [Avogadro-Discuss] (no subject)
> If I build a molecule from “File” > “Import” > “Fetch by chemical name…”, how > exactly is the molecule built? The structure is fetched via the NIH molecular resolver: https://cactus.nci.nih.gov/chemical/structure > How much can I trust the bond angle or bond length building this way? Personally, I'd highly suggest using force field minimization. In principal, the molecular geometries are built from CORINA, a package that uses crystal structure geometries. But I don't think I'd draw any conclusions other than "it's probably a reasonable starting geometry" -Geoff --- Prof. Geoffrey Hutchison Department of Chemistry University of Pittsburgh tel: (412) 648-0492 email: geo...@pitt.edu web: http://hutchison.chem.pitt.edu/-- Site24x7 APM Insight: Get Deep Visibility into Application Performance APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month Monitor end-to-end web transactions and take corrective actions now Troubleshoot faster and improve end-user experience. Signup Now! http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140___ Avogadro-Discuss mailing list Avogadro-Discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/avogadro-discuss
[Avogadro-Discuss] (no subject)
Dear Avogadro users, If I build a molecule from "File" > "Import" > "Fetch by chemical name.", how exactly is the molecule built? How much can I trust the bond angle or bond length building this way? Thank you very much. Best regards, Michael -- Site24x7 APM Insight: Get Deep Visibility into Application Performance APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month Monitor end-to-end web transactions and take corrective actions now Troubleshoot faster and improve end-user experience. Signup Now! http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140___ Avogadro-Discuss mailing list Avogadro-Discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/avogadro-discuss
