Thanks for the reply - this problem occurs in the builder.Build method before the force field optimization, where initial coordinates are given to each atom.
-Peter On Fri, Jul 20, 2012 at 8:02 AM, scott_m <js...@cam.ac.uk> wrote: > Gen3d does a steepest descent optimization, weighted rotor search and then a > conjugate gradients optimization (see > http://forums.openbabel.org/what-does-gen3d-do-under-the-hood-td3397296.html). > You might want to try a simple forcefield optimization to start with (like > steepest descent) and see how that works. > > > > > -- > View this message in context: > http://forums.openbabel.org/Problem-with-gen3D-tp4655296p4655300.html > Sent from the General discussion mailing list archive at Nabble.com. > > ------------------------------------------------------------------------------ > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. Discussions > will include endpoint security, mobile security and the latest in malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
