Right.
For this forcefield, we need energy function plots for each of the
contributions, to see if they behave as expected.
This has not been tested well.
We suspect that some of the functions do not behave robustly.
Cheers,
Christoph
[EMAIL PROTECTED] wrote:
> Ok as long as i use the "Ethane-TestFF-output.mol" which is found in the
> 'test' folder, everything seems to be fine. But only the slightest
> movement of one coordinate ( e.g. switching the third position after
> decimal point of one coordinate to '0' leads to an energy of about 100
> kcal/mol ) Chemdraw still calculates an energy value of 35 kcal/mol for
> this molecule, which is pretty much what I would have exspected.
>
> Using a Chemdraw minimized ethan i get energys around 900 kcal/mol.
> Chemdraw uses mm2 to minimize but this doesn't explain the big
> difference does it?
>
> What is it that i do wrong here?
>
> Im using the ForceFieldTest implementation of Violeta only that i pass
> the molecule to the function instead of reading it from a file ( because
> i do this earlier ).
>
> Greetings Alex
>
>
>
>
>
>
>
>
> Quoting Christoph Steinbeck <[EMAIL PROTECTED]>:
>
>> 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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>
--
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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