cxcalc averagemolecularpolarizability fails

 

cxcalc fails to calculate averagemolecularpolarizability for the follwing SMILE string :

cxcalc averagemolecularpolarizability "[H]C1N4CC(=C([H])C([H])([H])[H])C5([H])(C1([H])C([H])(OC(=O)C([H])([H])[H])C2C(=NC3C2C([H])C([H])C([H])C3([H]))C4([H])C5([H])([H]))"

Timelimit exceeded. Try to increase timelimit with option [timelimit]

And then it keeps running ...

 

Thanks,

Ralf.

 

JChem 5.3.8, Ubuntu 10.04

During polarizability calculation the 3D geometry of the structure is also calculated, and this leads to time limit (the error message comes from the 3D generator). We will examine how we can improve the speed of Generate3D on this structure.

Zsolt