> Then I recognized the OBFieldForce class (example used in the obenergy tool) > and I got rather large energy values in kJ/mol for molecules of at most 240 > amu. Finally I built in the energy minimizing step (using the > pFF->ConjugateGradients(10000)), but only the energy values of small > molecules became smaller - the larger molecules stayed at their high positive > energies (i.e. > 1e10).
You've gotten two good answers. The third would be -- what force field are you using? In principal, MMFF94 is intended to reproduce heats of formation, although Noel indicated a number of problems with this. I have no idea what UFF energies are supposed to indicate -- the paper suggests that relative energies are supposed to reproduce activation barriers, but I don't think that's been tested. If you really want fairly accurate heats of formation, I suggest a semiempirical quantum calculation, for example with MOPAC (e.g., AM1 or PM6) which has been specifically parameterized for such a task. BTW, if you read MOPAC output files with Open Babel, then the OBMol energy will reflect the heat of formation calculated by MOPAC. Best regards, -Geoff P.S. This particular property will be disappearing in Open Babel v3. Energy is a function of the computation method, not the molecule itself. ------------------------------------------------------------------------------ SOLARIS 10 is the OS for Data Centers - provides features such as DTrace, Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW http://p.sf.net/sfu/solaris-dev2dev _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
