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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--
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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