Dear Brian,
UFF is not used during MMFF94 minimization; I think you get that error
from a command that you execute before the MMFF minimization, which uses
UFF (my guess is that it happens when you call rdDistGeom.EmbedMolecule()).
Unfortunately, however, MMFF94 does not have parameters for boron, so
even if UFF succeded, MMFF94 would fail optimizing your molecule:
>>> from rdkit import Chem
>>> from rdkit.Chem import rdForceFieldHelpers
>>> mol = Chem.MolFromSmiles('[BH3]')
>>> rdForceFieldHelpers.MMFFHasAllMoleculeParams(mol)
False
Kind regards,
Paolo
On 21/10/2017 00:04, Bennion, Brian wrote:
Hello
In order to bypass errors in UFF typing I am using MMFF94 as a
minimization forcefield. However errors about UFF atom type are still
occurring for Boron.
staring MMFF94 minimization
CHEMBL2374533
[15:59:34] UFFTYPER: Unrecognized atom type: B_1 (26)
[15:59:34] UFFTYPER: Unrecognized atom type: B_1 (27)
staring MMFF94 minimization
CHEMBL115107
Not sure what things means? Is UFF atom typing just the default
behavior and there is no way around it?
Thanks
Brian
------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
_______________________________________________
Rdkit-discuss mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
_______________________________________________
Rdkit-discuss mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
