When I run conformational search for perflurooctanic acid (attachment t56.sdf), I got conformers where coordinates look strange (shifted ). Results are also attached. I'm using Marvin 126.96.36.199 and I was generating 100 conformers, with NORMAL optimization limit, diversity limit 0.1 and prehydrogenize = TRUE.
thank you for the report. Could you be more specific which conformer of the file t56conformers.sdf contains the unexpected coordinates?
It is recommend to enable Tools\Conformation\Conformers MMFF94 optimization if you are interested in conformational energy differences.
Actually conformers itself are fine, but all the coordinates are shifted far from the 0-point. For example: (396.9946 -429.2786-1397.6356 C). Since Y and Z coordinates now have no space between them I run into trouble when I try to parse MOPAC output.
I haven't seen this kind of behaviour with other molecules. Only this one.
I could not reproduce your shifted coordniates starting from t65.sdf in Marvin Sketch 188.8.131.52. However it does not mean that there is no bug. As a simple workaround before conformer generation could you please click on "Restore Defaults" button? After generating conformers you can easily check its coordinates in the Edit\Source menu of the popup molecule viewer window.