> I am struggling with the geometry optimization routine "obminimize" > within Open Babel. It works perfectly, but I wonder how I can put > the resulting structure back into a *.mol2 file, since the result > only appears in the command window.
You can redirect output to the terminal, e.g.: obminimize ... >out.mol2 > 1. Are there already semi-empirical calculation routines for > geometry optimization available such as AM1 etc.? No. I highly doubt we will ever implement quantum mechanics inside Open Babel. People have requested some level of molecular mechanics for handling conformer searching and 3D coordinate generation (e.g., from SMILES or InChI). If you're looking for semi-empirical QM, I suggest looking at packages like MOPAC2009. > 2. Which optimization method should I use, conjugate gradients or > steepest descent? Both lead to different results. Ultimately, they should lead to the same minimum geometry, although not necessarily with the same number of steps. If your geometry is far from a minimum, steepest descent is probably better than conjugate gradients. However, the latter is usually faster to converge to a minimum. Cheers, -Geoff ------------------------------------------------------------------------------ Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference _______________________________________________ OpenBabel-discuss mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
