No regular build due to fallback

User 036058eabf

26-02-2008 13:29:57


I'm getting this error when trying to get the 3d conformation of a particular molecule fragment:

No regular build due to fallback.

Clean failed.


What I'm doing is:

- Importing a molecule defined by a SMILES string; I'm using the PDB 2BE2 ligand as an example, for other ligands everything works;

- Finding all the rotatable bonds according to the Topology Analyser Plugin;

- Removing those bonds and converting the molecule to fragments;

- For each fragment, find the 3D conformation via the Conformer Plugin

The error occurs when running; I get that error and no conformation is generated. Although for other fragments of the same ligand it's ok.

The input ligand is:


The fragment which gives an error is:


Loading the fragment from the SMILES string and generating the conformation this way works well. Also generating the 2d conformation instead of 3d works.

I have attached a short program to show the problem.

Thank you!


ChemAxon 8b644e6bf4

26-02-2008 18:27:10


Thank you for the detailed description. The 3D calculation failed because a false CIS/TRANS stereo flag appeared in the fragment. This bug will be fixed in the next release, for the meantime you can work around this problem by manually deleting the C/T flags from the bonds:

for( int j = 0; j < newMol.getBondCount(); j++ ) {

MolBond bond = newMol.getBond( j );

bond.setFlags( 0, MolBond.CTUMASK );