Bob, The script I’m using is old. It predates your adding the charges to the extractable molfile. The production version I’m now using does have the charges in the extracted molfile, and it does draw the MEP of alkanes. The molfile is below. This is an easy work around that may not really be a work around. The complete MEP script that I use already assigns partial charges to the hydrogen halides because I think MMFF94 does not work with these binary compounds.
http://chemagic.com/molecules/models/methane.txt __Jmol-14_08241513413D 1 1.00000 0.00000 0 Jmol version 14.2.4_2014.08.03 2014-08-03 08:56 EXTRACT: ({0:4}) 5 4 0 0 0 0 1 V2000 0.00000 0.00000 0.00000 C 0 0 0 0 0 0 0.55410 0.79960 0.49650 H 0 0 0 0 0 0 0.68330 -0.81340 -0.25360 H 0 0 0 0 0 0 -0.77820 -0.37350 0.66920 H 0 0 0 0 0 0 -0.45930 0.38740 -0.91210 H 0 0 0 0 0 0 1 2 1 0 0 0 1 3 1 0 0 0 1 4 1 0 0 0 1 5 1 0 0 0 M END > <JMOL_PARTIAL_CHARGES> 5 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 Otis -- Otis Rothenberger o...@chemagic.com http://chemagic.com > On Aug 24, 2015, at 1:05 PM, Robert Hanson <hans...@stolaf.edu> wrote: > > I think that's been there forever. HC have 0 partial charge, so it is never > saved, then its absence is flagged. > ------------------------------------------------------------------------------ _______________________________________________ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
