Problem with conformer plugin

Hi,

I have two very similar molecules and I calculate their conformers using the following command line instruction:

./cxcalc conformers -m 200 -d 0.1 -l 1000 input.sdf > output.sdf

One molecule (1nvs_ligand.sdf, attached) gives rise to only one conformer, whilst the other molecule (1nvq_ligand.sdf, attached) gives rise to no conformers and the calculation finishes with a message about the time limit being exceeded.

I understand I only get one conformer for 1nvs because the diversity limit is pretty strict (0.5 Angstroms). However, why doesn't Marvin return at least the input conformer for the 1nvq ligand?

Thank you,

Juliette

Hi Juliette,

I run the same command to calculate the conformers of the attached molecules and the outputs were successfully generated (find attached); however, it took ~1 min for the 1nvq_ligand and  ~5 min for the 1nvs_ligand.

(cxcalc version 5.8.2)

Maybe your computer was overloaded, the memory was low for this calculation, so I suggest that you should increase the timelimit of conformer caluclation to obtain (better) results.

To answer your question:
The calculation will not retun the input structure as result/output: inputs can be 0D, 2D, or 3D molecules while the conformer output always results in 3D structure(s).

Best Regards,

Viktoria

vpalfi wrote:

Hi Juliette, I run the same command to calculate the conformers of the attached molecules and the outputs were successfully generated (find attached); however, it took ~1 min for the 1nvq_ligand and  ~5 min for the 1nvs_ligand. (cxcalc version 5.8.2) Maybe your computer was overloaded, the memory was low for this calculation, so I suggest that you should increase the timelimit of conformer caluclation to obtain (better) results. To answer your question: The calculation will not retun the input structure as result/output: inputs can be 0D, 2D, or 3D molecules while the conformer output always results in 3D structure(s). Best Regards, Viktoria

Hi Viktoria,

Thank you for the prompt reply. I was using an older version of cxcalc (5.5.0.1 I think). I have now downloaded 5.8.2 and it works as you have described - for all ligands where I was having problems, I now have no issues. 

Thanks again!

Juliette