I'm trying to generate conformers for a number of structures and am running into the following error when running cxcalc with the flags [ "lowestenergyconformer", "-x", "mmff94", "--maxconformers", "1","--multifrag","true"].
The error is:
"Consystency error in FragmentStore: conformer count mismatch"
I have attached some example structures with the issue. Any ideas?
We managed to reproduce the conformer generation problem. Yes, this is an iternal bug in our confomer generator module. We are going to fix it ASAP. However, the command also generates the conformer and outputs it to the standard output.
Thank you so much for the help. I just wanted to give more details on an errors that occasionally occurs with some of the molecules in that dataset I sent (for example with 5,10-Diaryl Mg-oxochlorin or TBP-meso-tera(4-COOMe-phenyl)-Zn).
This is an example error output: http://pastebin.com/raw.php?i=n4DbEnKw
Sorry to bother again! I just wanted to know if there had been any luck with the second error I posted? Any help would be more than appreciated.
we haven't managed to schedule the whole fix of the problem. However, we found a workaround that could help:
the issue of generating confomers for some molecules among the input were sensible to the order of the atoms. Please try to use the SMILES codes that appear in the error output or the SMILES format for conformer generation. Using this format can alter the order of the atoms, which might help to overcome the problem.
Let us know about the results.
When using the GUI, the following molecule unfortunately still fails conformer generation with the MMFF94 forcefield? Dreiding appears to work for some reason, however?
Yes, we managed to reproduce the problem and it might be MMFF94-related. However, currently we cannot put any effort on issues with the conformer generation. Thank you for reporting this bug. We will notify you if we resolve the problem.