Hi Eduardo,
Have you tried a python package called RMSD? Here is the link for this
package https://pypi.org/project/rmsd/. I have used this program to
calculate the RMSD between conformers and it works pretty well. You just
need to give the xyz matrices of each molecule as input. There are a few
examples on the Github page. I hope it helps.
Max Pinheiro Jr
Em ter., 9 de jun. de 2020 às 08:13, Eduardo Mayo <
eduardomayoya...@gmail.com> escreveu:
> Hi I'm trying to calculate the RMSD between conformers of the same
> molecules stores in separate mol file.
> I figured out a way:
>
> m1= Chem.FromMolFile('1.mol')
> m2= Chem.FromMolFile('2.mol')
>
> m1.AddConformer(M2.GetConformer(-1),1)
> AllChem.GetConformerRMS(m1,0,1)
>
> Is there another way??
>
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