Diversity limit causes Marvin conformer calculation to hang

User dd0280721c

08-09-2011 15:26:59


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.

Kind regards,


ChemAxon 8b644e6bf4

13-09-2011 16:02:42

Dear Juliette,


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

real    5m13.313s
user    0m0.015s
sys     0m0.015s

cxcalc conformers -m 70 -d 1.4 -l 90000 single_ligand.sdf > confs70.sdf 2>confs70.verbose.txt

real    8m11.480s
user    0m0.015s
sys     0m0.000s

If you have further questions please do not hesitate to ask them,