Dear Sereina and Paolo,
Thank you for your replies and they both seemed to correct the problem. I
really like to do it during the embedding of the molecule. cheers!
On Tue, Oct 8, 2019 at 12:34 PM Sereina <sereina.rini...@gmail.com> wrote:
> Hi Jorgen,
>
> Which version of RDKit are you using? The ETKDG conformer generator (which
> will keep sp2 centers flat) has become only recently the default. If you
> are using an older RDKit version, the following code should give you a flat
> aromatic system for the SMILES you provided in your example.
>
> m =
> 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’)
> mH = AllChem.AddHs(m)
> AllChem.EmbedMolecule(mH, params=AllChem.ETKDGv2())
>
> Best regards,
> Sereina
>
>
> On 8 Oct 2019, at 18:18, Paolo Tosco <paolo.tosco.m...@gmail.com> wrote:
>
> Hi Jorgen,
>
> use the MMFF94s variant of the forcefield if you wish to force trigonal
> nitrogens to be planar:
>
> AllChem.MMFFOptimizeMolecule(m2, mmffVariant="MMFF94s")
>
> More information here:
>
>
> https://doi.org/10.1002/(SICI)1096-987X(199905)20:7%3C720::AID-JCC7%3E3.0.CO;2-X
> Cheers,
> p.
>
> On 10/08/19 15:27, Jorgen Simonsen wrote:
>
> 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
>>
>>
>>
> _______________________________________________
> Rdkit-discuss mailing list
> Rdkit-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
>
>
_______________________________________________
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
