Hi Mark, have you tried a multi-link job in Gaussian, where each calculation relied on the result of the previous? I used to tunnel an imperfect input structure into a Dreiding forcefield in Gaussian, then read the result from a checkpoint file, do a semiempirical and then some higher level.
%chk=mol.chk #T dreiding Opt Test then #T mndo opt Geom=AllCheck test then #T B3LYP/6-31G(d) opt freq Test Geom=AllCheck Guess=Read The exact structure for the input file should be easy to find out. A robust model builder to get to an input is difficult to find. You might want to check open babel. One solution to get to a resonable input might be to replace all the Aluminum by something more common, do model building in Open Babel and replace back before going into Gaussian. I'm not sure if CDK will give you quick results because of lacking atom types. Cheers, Chris -- Dr. Christoph Steinbeck Head of Chemoinformatics and Metabolism European Bioinformatics Institute (EBI) Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD UK Phone +44 1223 49 2640 What is man but that lofty spirit - that sense of enterprise. ... Kirk, "I, Mudd," stardate 4513.3.. On 5 Jul 2011, at 22:52, Mark Holfelder wrote: > 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 > [email protected] > https://lists.sourceforge.net/lists/listinfo/cdk-user ------------------------------------------------------------------------------ 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 [email protected] https://lists.sourceforge.net/lists/listinfo/cdk-user
