Hey, my name is Mark Holfelder, and I'm working with the Bernstein group at Colorado State University on structure elucidation of some new Aluminium-Carbon clusters we've developed. As these are completely new substances, nothing is known about them except molecular formulae derived from Mass Spec data. So, I'm implementing a simulated annealing algorithm (Similar to the SENECA program, but unable to use Faulon's equations on bonds) to deduce the lowest energy structures. The algorithm is complete, but I'm currently using randomly generated coordinates to feed into Gaussian, the program we use for energy calculations. The random coordinates cause Gaussian to not converge when performing an RHF calculation, while using a Molecular Mechanics force field doesn't give good enough results. My first try was to use the ModelBuilder3D provided, but it fails as in the stack trace below. I've also tried using the StructureDiagramGenerator to generate 2D coordinates and just use a random z element, but it throws ArrayIndexOutOfBoundsExceptions occasionally, with the stack trace as below. The exception is not thrown every time the StructureDiagramGenerator is run. SimulatedAnnealer and runner are both my programs. Is there something that would cause these problems in the way that I'm building the molecule? I can attach my code if necessary. Also, failing something obvious that I should be doing and am not, are you aware of any heuristics that I could use to quickly generate rough 3D coordinates for my molecules? Thank you for your time.
For ModelBuilder3D: Could not final configure atom 2 due to org.openscience.cdk.exception.NoSuchAtomTypeException: Atom is unkown: Symbol:Al does not MATCH AtomType. HoseCode:Al-3;AlCC(&&,&,&&,&//) org.openscience.cdk.exception.CDKException: Could not final configure atom due to problems with force field at org.openscience.cdk.modeling.builder3d.ForceFieldConfigurator.assignAtomTyps(ForceFieldConfigurator.java:296) at org.openscience.cdk.modeling.builder3d.ModelBuilder3D.generate3DCoordinates(ModelBuilder3D.java:196) at SimulatedAnnealer.cost(SimulatedAnnealer.java:377) at SimulatedAnnealer.anneal(SimulatedAnnealer.java:72) at runner.main(runner.java:33) Caused by: org.openscience.cdk.exception.NoSuchAtomTypeException: Atom is unkown: Symbol:Al does not MATCH AtomType. HoseCode:Al-3;AlCC(&&,&,&&,&//) at org.openscience.cdk.modeling.builder3d.ForceFieldConfigurator.configureMM2BasedAtom(ForceFieldConfigurator.java:542) at org.openscience.cdk.modeling.builder3d.ForceFieldConfigurator.configureAtom(ForceFieldConfigurator.java:391) at org.openscience.cdk.modeling.builder3d.ForceFieldConfigurator.assignAtomTyps(ForceFieldConfigurator.java:293) ... 4 more Exception in thread "main" java.lang.NullPointerException at SimulatedAnnealer.cost(SimulatedAnnealer.java:397) at SimulatedAnnealer.anneal(SimulatedAnnealer.java:72) at runner.main(runner.java:33) For StructureDiagramGenerator: Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: -1 at org.openscience.cdk.AtomContainer.getAtom(AtomContainer.java:289) at org.openscience.cdk.AtomContainer.clone(AtomContainer.java:1596) at org.openscience.cdk.Molecule.clone(Molecule.java:105) at org.openscience.cdk.layout.StructureDiagramGenerator.setMolecule(StructureDiagramGenerator.java:138) at org.openscience.cdk.layout.StructureDiagramGenerator.setMolecule(StructureDiagramGenerator.java:223) at SimulatedAnnealer.cost(SimulatedAnnealer.java:369) at SimulatedAnnealer.anneal(SimulatedAnnealer.java:81) at runner.main(runner.java:33) ------------------------------------------------------------------------------ All of the data generated in your IT infrastructure is seriously valuable. Why? It contains a definitive record of application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-d2d-c2 _______________________________________________ Cdk-user mailing list Cdk-user@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/cdk-user