Dear Alex,
I have seen your example. I think that in this
particular case the problem is that the molecule has a
2D structure even if you give to the third coordinates
a zero. We also had the same result in these cases for
the MMFF94 energy calculation.
Best regards,
Violeta
--- [EMAIL PROTECTED] wrote:
> Hello Violeta,
>
> thank you very much for your answer - it helped me a
> lot but I have
> another problem now.
>
> Since you have written the ForceFieldTest class
> maybe you can help again.
>
> When first trying to use the ForceField package I
> accidentally made a
> bad molecule choice - with the molecule ( attachment
> )I had choosen,
> even your test classes fail.
>
> Is it a known issue of the Forcefield package that
> some molecules won't work?
>
> Plus I don't get the reason why it fails, the
> exception thrown is just: null
>
> I tried only few molecules so far but the attached
> one is the only one
> producing this problem.
>
> Have a nice weekend ;)
>
> Alex
>
>
>
>
>
>
> Quoting Violeta Labarta <[EMAIL PROTECTED]>:
>
> > Dear Alex,
> >
> > In ForceFieldTest you can find a method with name
> > testGetMMFF94EnergyOfAMolecule, that, I think does
> the
> > same what you want. I would try it.
> >
> > Best regards,
> >
> > Violeta
> >
> > --- [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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> >
> >
> >
> >
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