If you're only sampling 20 conformers, it's unlikely to be a global minima. It will usually be a lower energy conformer than what you started.
Does it need to be further optimized? Well, usually yes, but it depends - the weighted search option does minimize with the MMFF94 force field by default - but whether it needs further optimization depends on your needs. My research group, for example, typically does density functional or other quantum chemical calculation - so a MMFF94 geometry is only a starting point. Hope that helps, -Geoff --- Prof. Geoffrey Hutchison Department of Chemistry University of Pittsburgh tel: (412) 648-0492 email: geo...@pitt.edu twitter: @ghutchis web: https://hutchison.chem.pitt.edu/ > On Sep 18, 2019, at 3:37 AM, 20520181152...@stu.xmu.edu.cn wrote: > > Thank you for reading this email.I have a question to confirm: > I want to get the 3D coordinates of the molecules,after operations just like > your example: > > obabel ligand.babel.smi -O ligand.babel.sdf --gen3d --conformer > --nconf 20 --weighted > > > > Can we think of this conformation as the most stable > conformation of the molecule which is the global minimum conformation of the > molecule? Does it need to be optimized if I need use the conformation for > futher computer ? > > > > I shall be most grateful if I receive your letter ! > > > > > _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
_______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
