Hello Violeta and Christoph,
thank you very much for your answers. From what you have said so far I
think that I can't use the forcefield for my purpose at the moment,
because most times my molecules start from horrible conformations ;).
On the other hand, time is running thus I can't go deeper into really
testing the forcefield systematically.
Thanks again for your your time and effort
Cheers,
Alex
Christoph Steinbeck schrieb:
> Alex,
>
> I'm almost sure that there are still flaws in the implementation of the
> energy function and certainly in the minimization.
> To the best of my knowledge, people use forcefield energy function and
> certainly minimizers only if they are already at a decent geometry.
>
> Here, we currently use the energy function with an evolutionary
> algorithm. We set the molecule up in internal coordinates with all the
> angles and bond length set to MMFF94 default values and the dihedrals
> such that they yield an extended conformation. Rings are modelled from
> templates. Minimizing the energy function leads to a good geometry. EA
> parameters still need tweaking, though.
>
> This seems to indicate that the force field works decently within it's
> domain.
> I don't know
> a) if it does anything reasonable if you start for example with a 2D
> structure.
> b) whether the energy values that it outputs are meaningful.
>
> As I already said: Violeta laid the ground work and now people who want
> to use it need to do the tedious fixing and optimization tasks.
>
> Cheers,
>
> Chris
>
> Violeta Labarta wrote:
>
>> 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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>>
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