Hi list, Good evening to all of you. Once again I need to ask you about something related to the forcefields and in particular MMFF94.
I looked at the validation for the MMFF94 OpenBabel implementation that Tim uploaded at http://home.scarlet.be/timvdm/MMFF94_validation_output.gz I found the dataset he used for that validation is different from the forcefields.sdf dataset that is currently used in the MMFF94 nightly build validation. So I went on to fetch the molecules directly from CCL.NET (http://www.ccl.net/cca/data/MMFF94) The problem is that there I found two slightly different datasets: MMFF94_dative.mol2 and MMFF94_hypervalent.mol2 . Which one of them is the one I should be using? I guess I am not using the appropriate one because when running obminimize against any of those I can't get any output: $ obminimize -ff mmff94 MMFF94_hypervalent.mol2 $ obminimize -ff mmff94 MMFF94_dative.mol2 Reason why I am asking you this, is because although the dataset in forcefield.sdf is good for validation, I will like to build a larger dataset for profiling purposes. A preliminar analysis of the profiling tool(I am using OProfile) is showing that the most intensive computation is occurring inside forcefield.cpp rather than forcefieldmmff94.cpp which is contrary to what I was initially expecting. Have a good weekend, -- Omar Valerio M. ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
