Small atomic displacements can cause large forcefield energy differences.
Computing molecular-mechanics energies from exactly the same coordinates
using two different force-fields is probably not a reasonable procedure.

It would be better to do an energy minimization with the two force fields
separately and live with the differing coordinates. Often the coordinate
differences will be small, but there are situations in which forcefield X
gives no conformation that is close to a minimized conformation obtained
from forcefield Y.

-P.

On Thu, Feb 9, 2017 at 11:48 AM, Méliné Simsir <meline.sim...@gmail.com>
wrote:

> Dear all,
>
> I'm still a beginner with Rdkit, and I’m having a hard time calculating
> the energy of conformers.
> I think I have read all the topics on the subject, but I might have missed
> something.
> Here is a shorten version of a code I wrote thanks to all the information
> I could find here.
>
> from rdkit import Chem
> from rdkit.Chem import AllChem
> from rdkit.Chem import rdmolops
>
> mols = Chem.SDMolSupplier('test_3c.sdf')
>
> for mol in mols:
>     # UFF
>     ffu = AllChem.UFFGetMoleculeForceField(mol)
>     energy_value_U = ffu.CalcEnergy()
>     print(energy_value_U)
>     # MMFF
>     mol = rdmolops.AddHs(mol, addCoords = True)
>     mp = AllChem.MMFFGetMoleculeProperties(mol)
>     ffm = AllChem.MMFFGetMoleculeForceField(mol, mp)
>     energy_value_M = ffm.CalcEnergy()
>     print(energy_value_M)
>
>
> My problem is that I get weird energy values (not all the time I think,
> but too often). Either too high or too low. And i don't get why.
> I would like to get the energy of my ligand as he is. Without changing
> it's conformation at all. That's why I don't use the minimization function,
> or optimization. First I also didn't add the hydrogen, but thanks to one of
> Paolo Tosco's code (mmffEnergyTerms.py), I saw that H are not included even
> if they are in the sdf file. But, I still have some weird values i think.
>
> Here three examples:
> GNP_1CIP : -305.2896 kcal/mol (MMFF, with H added)
>             -46.4812 kcal/mol (MMFF, without H add)
>             278.6606 kcal/mol (UFF)
>
> SAM_2IGT: 1675.9951 (MMFF, with H added)
>             151.6481 (MMFF, without H add)
>             217.1217 (UFF)
>
> ACP_3A1C: 222.9396 (MMFF, with H added)
>             269.151 (MMFF, without H add)
>             217.1217 (UFF)
>
> Regards,
> Méliné
>
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