Re: [Rdkit-discuss] UFFTYPE error in MMFF minimization

[Paolo T. <pao...@un...>]

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
>
>
>
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