Standardization error and How to standardize those ?

Hi !

I am trying to standardize a list of structures and it appears that some structures error in the transformations. (the marvin version is 5.3.0) Those structures are in the attachment(SDF file).

The standardize command is:

standardize 8mol.sdf -c addexplicitH..aromatize..clean:3 -f sdf -o 8molop.sdf

and the error are:

Consystency error in FragmentStore: conformer count mismatch
Consystency error in FragmentStore: conformer count mismatch
Consystency error in FragmentStore: conformer count mismatch
Consystency error in FragmentStore: conformer count mismatch
Consystency error in FragmentStore: conformer count mismatch
Consystency error in FragmentStore: conformer count mismatch
Clean failed.
[H]O[C@]1([H])OC(=O)[C@]23C([H])([H])[C@@]12C(C([H])=O)=C([H])[C@@]1(O[H])C([H])
([H])C(C([H])([H])[H])(C([H])([H])[H])C([H])([H])C31[H]

Consystency error in FragmentStore: conformer count mismatch
Consystency error in FragmentStore: conformer count mismatch
Consystency error in FragmentStore: conformer count mismatch
Consystency error in FragmentStore: conformer count mismatch
Consystency error in FragmentStore: conformer count mismatch
Consystency error in FragmentStore: conformer count mismatch
Clean failed.
Cl[H].[H]N([H])[C@@]([H])(C(=O)N([H])[C@]1([H])C(=O)[N@]2[C@@]1([H])SC(C([H])([H
])[H])(C([H])([H])[H])[C@]2([H])C(=O)OC([H])([H])c1oc(=O)oc1C([H])([H])[H])c1c([
H])c([H])c([H])c([H])c1[H]
Timelimit exceeded. Try to increase timelimit with option [timelimit]
Consystency error in FragmentStore: conformer count mismatch
Consystency error in FragmentStore: conformer count mismatch
Consystency error in FragmentStore: conformer count mismatch
Consystency error in FragmentStore: conformer count mismatch
Consystency error in FragmentStore: conformer count mismatch
Consystency error in FragmentStore: conformer count mismatch
Clean failed.
[H]OC(=O)[C@]1([H])[N@]2C(=O)C([H])(N([H])C(=O)[C@]([H])(N([H])C(=O)N3C(=O)C(=O)
N(C([H])([H])C([H])([H])[H])C([H])([H])C3([H])[H])c3c([H])c([H])c([H])c([H])c3[H
])[C@]2([H])SC1(C([H])([H])[H])C([H])([H])[H]
Clean failed.
[H]OC([H])([H])[C@]12O[C@]1([H])[C@@]1([H])[C@]3([H])O[C@@]4(O[C@@]3(C(=C([H])[H
])C([H])([H])[H])[C@]([H])(OC(=O)C(\[H])=C([H])\C([H])=C(/[H])c3c([H])c([H])c([H
])c([H])c3[H])[C@@]([H])(C([H])([H])[H])[C@]1(O4)[C@]1([H])C([H])=C(C(=O)[C@@]1(
O[H])[C@]2([H])O[H])C([H])([H])[H])c1c([H])c([H])c([H])c([H])c1[H]
Timelimit exceeded. Try to increase timelimit with option [timelimit]
Timelimit exceeded. Try to increase timelimit with option [timelimit]

Those structures can not be optimized, why? and how  to solve the problem?

Thanks a lot for your assist !

 

Hi,

 

Thanks for the post.  The first attached structure seems to have revealed a bug in 3D coordinate generation. We will look into it and get back to you soon.

However 4 of the 8 structures have 3D coordinates and all of them contains strange artifacts. This may lead to invalid stereo specification which can not be fulfilled with a valid structure. A gradient optimization (which is not stereo aware) yields valid conformers which then can be converted to 2D and back to 3D.

May I ask where the 3D coordinates came from for these 4 structures?

 

Regards,

Gabor