cxcalc lowestenergyconformer

Hi!

I tried to generate 3D structures with cxcalc by

cat smifile.smi | cxcalc majormicrospecies -H 7.4 -f sdf | cxcalc lowestenergyconformer

This command produces 3D structures, but it does not generate the conformer with the lowest energy for example in the case of allene (C=C=C). There is a thread about this molecule here: https://www.chemaxon.com/forum/ftopic5714.html

Is it possible to change the energy minimization rotine used by cxcalc, that it uses the hyperfine criterion?

kind regards

Sören

Hi Sören,

 

Sorry for the late answer! Use option "-e" to do hyperfine in cxcalc. To set very strict optimization limit use "-O 3". To get a list of options available to conformers plugin use option "-h"

To get correct allene with hyperfine:

cxcalc "C=C=C"  conformers -e 

 

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

 

Regards,

Gabor