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 <mailto: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 list
Rdkit-discuss@lists.sourceforge.net
<mailto: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
