I would like to print out the warnings when calculating the pKa values of the molecules to my output but i see it printed to the console but not the output file. How can i print it to the output file as well?
/Applications/ChemAxon/MarvinBeans/bin/cxcalc -v --log-level warning -o results pKa -i 0 -x 9 -a 5 -b 5 -m macro molfiles/25802.mol
The only way to direct the errors and warnings of cxcalc to a file is to use the --log <file> option. That creates an SD file by default, containing e.g. the error message as an <ERROR> property. Otherwise cxcalc directs the log results to the console.
You can find out about all options of cxcalc by running cxcalc -h.
I hope this helps.