MMFF94 optimized structure

 

Hello!

I'm trying to get MMFF94 optimized structure and my code is something like that:

ConformerPlugin plugin = new ConformerPlugin();
		
		try {

			Molecule mol = MarvinConvertor.convert(str);
			// set target molecule
			mol.clean(3, null, null);
			plugin.setMolecule(mol);
			
			plugin.setMMFF94Optimization(true);
							
			// set parameters for calculation
						
			plugin.setDiversity(diversity);
			plugin.setTimelimit(time);
			plugin.setPrehydrogenize(preHydro);
			plugin.setOptimization(optLevel);
			
			// run the calculation
			plugin.run();
			
			if (plugin.isOK()) {

				// get results
								
				Molecule mmff94_mol = plugin.getMMFF94OptimizedStrucutre();
				System.out.println(mmff94_mol);
					

 But unfortunatly result is empty (null) molecule. Does i'm missing something here?

 

Best regards,

Geven

Hi Geven,

This will work:

public static void main(String[] args) throws Exception {

	ConformerPlugin plugin = new ConformerPlugin();
	Molecule mol = MolImporter.importMol("CC(=O)[N+]([O-])(c1cc(sc1C(N)=O)C(C)(C)C)c1ccc(OCCN2CCOCC2)c2ccccc12");
	
	// set target molecule
	plugin.setMolecule(mol);

	// set parameters for calculation
	plugin.setLowestEnergyConformerCalculation(true);
	plugin.setMMFF94Optimization(true);
	plugin.setPrehydrogenize(true);

	// run the calculation
	if (plugin.run()) {
	    // get results
	    Molecule mmff94_mol = plugin.getMMFF94OptimizedStrucutre();
	    System.out.println(mmff94_mol.toFormat("mrv"));
	}
}

plugin.setLowestEnergyConformerCalculation(true) should be turned on, MMF94 optimization works only in this case.

Zsolt