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
>>
>>
>>
>> -------------------------------------------------------------------------
>> This SF.net email is sponsored by: Splunk Inc.
>> Still grepping through log files to find problems? Stop.
>> Now Search log events and configuration files using AJAX and a browser.
>> Download your FREE copy of Splunk now >> http://get.splunk.com/
>> _______________________________________________
>> Cdk-user mailing list
>> [email protected]
>> https://lists.sourceforge.net/lists/listinfo/cdk-user
>
>
> --
> 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..
>
> -------------------------------------------------------------------------
> This SF.net email is sponsored by: Splunk Inc.
> Still grepping through log files to find problems? Stop.
> Now Search log events and configuration files using AJAX and a browser.
> Download your FREE copy of Splunk now >> http://get.splunk.com/
> _______________________________________________
> Cdk-user mailing list
> [email protected]
> https://lists.sourceforge.net/lists/listinfo/cdk-user
>
-------------------------------------------------------------------------
This SF.net email is sponsored by: Splunk Inc.
Still grepping through log files to find problems? Stop.
Now Search log events and configuration files using AJAX and a browser.
Download your FREE copy of Splunk now >> http://get.splunk.com/
_______________________________________________
Cdk-user mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/cdk-user
