cxcalc lowestenergyconformer

User 187e4c3b19

28-09-2011 08:47:19


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:

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

kind regards


ChemAxon 8b644e6bf4

05-10-2011 10:20:24

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!