> 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?
Avogadro uses Open Babel. So there is no difference in implementation. But, as Noel said, Avogadro would generate 3D coordinates for 2D structures and add hydrogens. You didn't mention if this were the case. Also, I wouldn't use the Ghemical force field. I'd recommend MMFF94 for general drug-like molecules, or UFF if the molecules include elements outside the MMFF94 parameterization (e.g., selenium). Hope that helps, -Geoff ------------------------------------------------------------------------------ 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
