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)
------------------------------------------------------------------------------
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