Re: [Cdk-user] forcefields - computing energy of given moelcule

[<Kl...@bi...>]

Ok as long as i use the "Ethane-TestFF-output.mol" which is found in =20
the 'test' folder, everything seems to be fine. But only the slightest =20
movement of one coordinate ( e.g. switching the third position after =20
decimal point of one coordinate to '0' leads to an energy of about 100 =20
kcal/mol ) Chemdraw still calculates an energy value of 35 kcal/mol =20
for this molecule, which is pretty much what I would have exspected.

Using a Chemdraw minimized ethan i get energys around 900 kcal/mol. =20
Chemdraw uses mm2 to minimize but this doesn't explain the big =20
difference does it?

What is it that i do wrong here?

Im using the ForceFieldTest implementation of Violeta only that i pass =20
the molecule to the function instead of reading it from a file ( =20
because i do this earlier ).

Greetings Alex








Quoting Christoph Steinbeck <er...@do...>:

> 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
>
> Kl...@bi... 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 =3D new MMFF94BasedParameterSetReader();
>>          PR.readParameterSets();
>>          EF =3D 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.setMMFF94BondStret=
chingParameters(BondStretching.java:103)
>>          at
>> org.openscience.cdk.modeling.forcefield.MMFF94EnergyFunction.<init>(MMFF9=
4EnergyFunction.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
>
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