I'm using MarvinBeans on the command line, using the following:
/home/pradon/ChemAxon/MarvinBeans/bin/cxcalc conformers -m 200 -d 1.4 -l 90000 single_ligand.sdf > all_conformers.sdf
When I set the diversity limit to 0.5, the calculation runs fine, but when I set it to 1.4 as in the command line above, the calculation hangs and no conformers are produced. Could you please tell me if you can reproduce my error and if so how to fix it? Is there a range of values possible for the diversity limit?
I also attach my ligand file.
Sorry for the late answer. In the upcomming 5.7 release a verbose mode will be added to Generate3D which helps to follow long executions. This revealed that using 1.4 diversity value around 60 conformers are generated in a considerable running time.
The recommended solution is to decrease required conformer count parameter (to 60-65 for the attached structure). When 5.7 release will be out the implemented verbose mode can be used to estimate a suitable conformer count parameter.
A brief introduction to Generate3D (usage and inner workings) can be found at https://docs.google.com/document/pub?id=1dgaNFWpBNqexlTRMmWF48II9qkL9e8ALdyFpoIlJfUY
A tracker topic where notifications on the major modification of this document can be found https://www.chemaxon.com/forum/ftopic8016.html
Outputs (generated conformers and verbose outputs) from the following runs (using a development version) are attached:
time cxcalc conformers -m 60 -d 1.4 -l 90000 single_ligand.sdf > confs60.sdf 2>confs60.verbose.txt
cxcalc conformers -m 70 -d 1.4 -l 90000 single_ligand.sdf > confs70.sdf 2>confs70.verbose.txt
If you have further questions please do not hesitate to ask them,