If the original structures are 2D, then the first thing you should make a 3D structure with --gen3d.
- Noel On 15 December 2012 07:33, 赖仁福 <lrf1...@gmail.com> wrote: > Hi All > > I am using the openbabel command line for generating 3D conformer for s set > of mol2 molecule database, and then use the database for a virtual > screening. i made a shell by the following commands: > #! /bin/bash > > for f in *.mol2; do > obminimize -ff Ghemical -n 10000 $f (minimize the energy by Ghemical force > field, set up 10000 as max steps) > obconformer 50 1000 $f >Meg/$f (generate best of conformer out of 50 after > 1000 geometry optimization steps, and save in fold Meg with same file name) > done > > this question is that after this process, the result is totally difference > with the results of another software named Avogadro (use the same Ghemical > force field for energy minimization). > > i want to figure out how the difference came out? should they be same since > their use same force field for calculation? > > Mac > > ------------------------------------------------------------------------------ > LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial > Remotely access PCs and mobile devices and provide instant support > Improve your efficiency, and focus on delivering more value-add services > Discover what IT Professionals Know. Rescue delivers > http://p.sf.net/sfu/logmein_12329d2d > _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > ------------------------------------------------------------------------------ LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial Remotely access PCs and mobile devices and provide instant support Improve your efficiency, and focus on delivering more value-add services Discover what IT Professionals Know. Rescue delivers http://p.sf.net/sfu/logmein_12329d2d _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
