Cheers Paolo,

It looks like that it keeps sp3 as the optimal geometry and not sp2.
The optimization did converge :

AllChem.MMFFOptimizeMolecule(m2,)

#returned 1

I think it is getting the types wrong or I have to specify the types?



On Tue, Oct 8, 2019 at 10:10 AM Paolo Tosco <paolo.tosco.m...@gmail.com>
wrote:

> Hi Jorgen,
>
> optimizing your molecule geometry with UFF or MMFF should fix the problem:
>
> AllChem.UFFOptimizeMolecule(m2)
>
> or
>
> AllChem.MMFFFFOptimizeMolecule(m2)
>
> see rdkit.Chem.rdForceFieldHelpers.UFFOptimizeMolecule
> <https://www.rdkit.org/docs/source/rdkit.Chem.rdForceFieldHelpers.html?highlight=optimize#rdkit.Chem.rdForceFieldHelpers.UFFOptimizeMolecule>
> or rdkit.Chem.rdForceFieldHelpers.MMFFOptimizeMolecule
> <https://www.rdkit.org/docs/source/rdkit.Chem.rdForceFieldHelpers.html?highlight=optimize#rdkit.Chem.rdForceFieldHelpers.MMFFOptimizeMolecule>
> .
>
> Cheers,
> p.
>
> On 10/08/19 14:41, Jorgen Simonsen wrote:
>
> Hi all,
>
> I am trying to built 3D structures from SMILES which for most of the
> molecules works fine - I get the SMILES from pubchem ('canonical_smiles'
> and 'isomeric_smiles') but some of the molecules they hydrogens are not
> added correctly and are out of plane - e.g. amide group in ATP ( see below
> for an example or arginine in a peptide).
>
> I use the following code to generate the 3D structure :
>
> from rdkit import Chem
> from rdkit.Chem import AllChem
> m1 =
> Chem.MolFromSmiles('C1=NC(=C2C(=N1)N(C=N2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N')
>
> m2 = Chem.AddHs(m1)
> AllChem.EmbedMolecule(m2)
>
> w = Chem.SDWriter('foo.sdf')
> w.write(m2)
>
> # or to mol file
>
> print(Chem.MolToMolBlock(m2),file=open('foo.mol','w+'))
>
> How to insure that the atomtype are correct ?
>
> Thanks in advance
>
> Best
> Jorgen
>
>
>
>
>
>
>
>
>
>
>
> _______________________________________________
> Rdkit-discuss mailing 
> listRdkit-discuss@lists.sourceforge.nethttps://lists.sourceforge.net/lists/listinfo/rdkit-discuss
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>
>
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