Ionization state SDF file molecule for given pH

Hi,

I wanted to find out the exact ionization state for all molecule under SDF file. I have 10000 molecule in that SDF file and i want know the exact ionization state for each molecule at pH 7.00. Usually i perform this task manually in marvin sketch for individual molecule. But it is very difficult to do this job individually for all 10000 molecule .

More precisely, how i find exact ionization state for all molecule in SDF file and which will produce another sdf file contains that exact ionization state.

 

Thank you.. 

Hello,

You can use our command line tool cxcalc to run calculations on sdf files and generate output files which contains the results of the calculations. 

This will look something like this in command line :

cxcalc -[output format] -o [output file name] [plugin] [plugin options] [input filename]

 

I hope this helps.

Best regards,

Tamas Fazekas-Vigh