I am importing the canonical SMILES string:
C=CC1C(C)C2=C(c3ccccc3)c3n4[Fe+2]56N2C1=Cc1c(C)c(c(n51)C=c1n6c(=Cc4c(c3C=C)C )c(c1CCC(=O)O)C)CCC(=O)O and saving to MOL2 format with 3D coordinates selected. During energy minimization (conjugate gradients, 200 iterations, 0.1 energy delta for convergence), MMF94 and UFF don't seem to result in downhill travel, and leave the molecule flat. However, GAFF and GCHEMICAL seem to result in appropriate changes as the energy goes downhill. I elected to minimize without conformer searching: '>>>>>>>>>>>>>>>>>>W/o Conformer search pFF.EnableCutOff(True) pFF.SetVDWCutOff(10.0) pFF.SetElectrostaticCutOff(20.0) pFF.SetUpdateFrequency(10) ' // update non-bonded distances infrequently pFF.ConjugateGradients(250, 0.0001) pFF.UpdateCoordinates(Mol) '>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Do you think that, for MMF94, I need to use conformer searching? Also, are GAFF or GCHEMICAL libraries available in OB.Net?
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