> *The -f -l option doesn't work when you want multiple files as output (-m)
No, because they're somewhat at cross-purposes. My suggestion would be something like this: obabel -f X -l Y [other options] -ocopy | obabel -m [.. other options] You can use the "copy" pseudo-format to allow filtering of an input file (e.g., -f -l, -S, etc.) and then output with another command using a pipe. > *I'm guessing -h and -p are redundant so I only need to use one. This was > never truly touched upon in the documentation. Yes, -h implies adding all hydrogens, while -p implies pH selective hydrogens. > * --gen3D adds hydrogens by default so I was wondering if it was redundant > with -h or -p. Furthermore I was wondering what --gen3D actually does, > because it seems that it optimizes bond lengths and angles. Is it simply a > "geometric optimization" or is there an energy minimization? What is a geometric optimization if not a minimization of the energy? > * is minimization redundant with gen3D? No. gen3D creates a rough geometry, then does a quick (500 step) minimization, then a quick conformer search, then another quick minimization. Further minimization may still be useful. > * I'm having issues with gen3D, it gives me error messages with "steplength", > I forget the exact wording but what does steplength do? That's a warning that the initial rough geometry was a bit weird. It's not an error. Hope that helps, -Geoff --- Prof. Geoffrey Hutchison Department of Chemistry University of Pittsburgh tel: (412) 648-0492 email: geo...@pitt.edu web: http://hutchison.chem.pitt.edu/ ------------------------------------------------------------------------------ Slashdot TV. Video for Nerds. Stuff that Matters. http://pubads.g.doubleclick.net/gampad/clk?id=160591471&iu=/4140/ostg.clktrk _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
