On 09/18/2013 12:32 PM, Geoffrey Hutchison wrote: >> What is the default model used to compute the partial charges? > > Gasteiger. The mol2 output actually will say this. > >> Is there a way to control which one to use? > > > Of course: > > obabel --partialcharge MMFF94 … > > obabel -L charges # gives a list of the installed charge models > > Hmm, this needs to go into the next documentation update.
I confirm the output files always contain USER_CHARGES instead of the actual charge model that was asked to Open Babel. This is a bug, it doesn't respect the mol2 file format. I used commands such as those: obabel input.mol2 -Ooutput.gasteiger.mol2 --partialcharge gasteiger obabel input.mol2 -Ooutput.mmff94.mol2 --partialcharge mmff94 obabel input.mol2 -Ooutput.qeq.mol2 --partialcharge qeq obabel input.mol2 -Ooutput.qtpie.mol2 --partialcharge qtpie I use "Open Babel 2.3.0 -- Dec 17 2011 -- 16:15:10" from Ubuntu's package: ii openbabel 2.3.0+dfsg-3ubuntu3 Regards, F. ------------------------------------------------------------------------------ October Webinars: Code for Performance Free Intel webinars can help you accelerate application performance. Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from the latest Intel processors and coprocessors. See abstracts and register > http://pubads.g.doubleclick.net/gampad/clk?id=60135991&iu=/4140/ostg.clktrk _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
