People from various branches of chemistry have contributed to OpenBabel and the terms they use are not always compatible.
If you were expecting numbers like Enthalpy of Formation of methane at 300K to be about -74.8 kJ/mol, and wanting to estimate that for any molecule (or even handle it), I am afraid OpenBabel cannot help much at present. Elsewhere I have implemented thermodynamic property estimation from structure by group additivity and have in mind to port it to OpenBabel. However I have had this in mind for a very long time, so don't hold your breath. OBMol::GetEnergy() accesses data previously input from from, for example, Gaussian format. It is a zero-point energy on a computational chemistry baseline (is this separated electrons and nuclei?) and needs much reworking to put it on the thermodynamic basis I think you are interested in. Chris Daniel Hoegerl wrote: > Hi everyone, > > I'll immediately start, so: > > I'm trying to calculate the gibbs energy of a molecule, and first found the > class OBMol and it's method "GetEnergy()". I'm creating the OBMol object from > a SMILES string. However, GetEnergy() allways (well, I tried with a lot > molecules) returns 0.0. > > 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). > > So my first question is: what is this energy in a chemical sense - I thought > it to be the "heat of formation", oder the free enthalpy or even the gibbs > energy!? > > And why is OBMol->GetEnergy() always 0.0? ------------------------------------------------------------------------------ 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
