User 9b067d2e85
23-11-2011 00:27:29
I am getting the following error:
Consystency error in FragmentStore: conformer count mismatch
Clean failed.
OC1=N[C@]2(C[N@]3CC[C@H]2CC3)C(=O)N1CN(CC1=CC=CC=C1)C1=CC=CC=C1
The files are attached below.
I am loading the original molecule, running the protomer/tautomer/stereoisomer plugins and get a set of mols, one of which is attached below (problemMolecule.sdf) which I then try to clean into 3D using the following code, but fails, getting the above error.
Molecule stereoisomer; // assuming this actually holds the molecule
stereoisomer.clean(3, "S{fast}");
Thanks
User a9d76a1173
23-11-2011 16:18:23
dgarden wrote: |
I am getting the following error:
Consystency error in FragmentStore: conformer count mismatch
Clean failed.
OC1=N[C@]2(C[N@]3CC[C@H]2CC3)C(=O)N1CN(CC1=CC=CC=C1)C1=CC=CC=C1
The files are attached below.
I am loading the original molecule, running the protomer/tautomer/stereoisomer plugins and get a set of mols, one of which is attached below (problemMolecule.sdf) which I then try to clean into 3D using the following code, but fails, getting the above error.
Molecule stereoisomer; // assuming this actually holds the molecule
stereoisomer.clean(3, "S{fast}");
Thanks
|
Clean 3D fail for some molecules. I ran into this problem very often when generating coordinates for compounds downloaded from pubchem. Try a gradient optimization before generating conformers. stereoisomer.clean(3, "[c]{2}[o]{1}{0}"); should work.
Lochana
User 9b067d2e85
23-11-2011 23:02:56
Thanks for the help, that fixed the problem. In the reply you said "[c]{2}[o]{1}{0}", but in the email I got it says "{2}{1}{0}," what is the difference? I can't seem to find the documentation on these specific arguments, could you point me in the right direction? I've only seen documents on S{fast} and S{fine}.
Thanks again.