Hi Masaaki! Well thanks for testing the 3D CDK modelbuilder. Well the problem you have just met is the one I have been working on to recover.
Well, the 3d builder assigns bond lengths and angles, ... based on two forcefields : MM2 and MMFF94. To do this it has to first assign the correct force field atom types to each atom and then look up the corresponding length and angles from the force field parameter file, in your case the MM2 .prm file. The problem in your case is that the atom type configurator method doesnt assign the correct types to the atoms and therefore some bond will not be found in the .prm file. The other problem is with the template handler : it doesnt recognize the rings well yet :( First I suggest that you should use the MMFF94 force field with the following "constructor" parameters : TemplateHandler3D tHandler3d = TemplateHandler3D.getInstance(); String forceFieldName = "mmff94"; ModelBuilder3D modelBuilder3d = ModelBuilder3D.getInstance(tHandler3d, forceFieldName); Please rerun the calculation and inform us with the detailed output. I can fix the bad atom type assignments for you then. Daniel ------------------------------------------------------------------------------ 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/ _______________________________________________ Cdk-user mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/cdk-user
