In addition to what Violeta already said, I can say that we are
definitely using this forcefield implementation for energy calculation.
We currently use it with a genetic algorithm for minimization which
finds the correct minimum, meaning that the energy calculation is
largely correct. There maybe some problems with bond stretching farer
away from the equilibrium, but if you start with a reasonable structure,
you should be fine.
Cheers,
Chris
[EMAIL PROTECTED] wrote:
> Hello,
>
> I am trying to get the actual energy of a given Molecule using MMFF94.
> Is this possible at all? Just to avoid missunderstandings: I don't
> want to minimize the energy.
>
> What I have been trying to do so far is the following:
> ____________________________________________________________
>
> public class EnergyCalculations {
>
> MMFF94BasedParameterSetReader PR;
> MMFF94EnergyFunction EF;
>
> public EnergyCalculations() {
>
> }
>
> public double getMoleculeEnergy(Molecule mol) throws Exception {
>
> PR = new MMFF94BasedParameterSetReader();
> PR.readParameterSets();
> EF = new MMFF94EnergyFunction(mol, PR.getParamterSet());
> return EF.energy();
> }
>
> _____________________________________________________________
>
> I am not sure if this really is what i want, but however it doesnt
> work. I get a NullPointerException and I'm not sure why...?
>
> In detail:
>
> Exception in thread "Main java.lang.NullPointerException
> at
> org.openscience.cdk.modeling.forcefield.BondStretching.setMMFF94BondStretchingParameters(BondStretching.java:103)
> at
> org.openscience.cdk.modeling.forcefield.MMFF94EnergyFunction.<init>(MMFF94EnergyFunction.java:46)
> at
> test.EnergyCalculations.getMoleculeEnergy(EnergyCalculations.java:62)
> at test.Main.<init>(Main.java:107)
> at test.Main.main(Main.java:252)
>
> Maybe someone who already worked with the implemented ForceFields can
> share some of his experienence with me or tell me what i am doing
> wrong here.
>
> Thank you for any help &
>
> best regards
>
> Alex Klenner
>
>
>
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--
PD Dr. Christoph Steinbeck
Lecturer in Chemoinformatics
Univ. Tuebingen, WSI-RA, Sand 1, D-72076 Tuebingen, Germany
Phone: (+49/0) 7071-29-78978 Fax: (+49/0) 7071-29-5091
What is man but that lofty spirit - that sense of enterprise.
... Kirk, "I, Mudd," stardate 4513.3..
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