Problem Generating pKa Training Library

User d01a87829a

18-12-2015 20:00:34


I have been having trouble generating a pKa training library. 

I made an SDF file using the example pka_trainingset.sdf included with the program, and edited the table using Discovery Studio. When I open pka_trainingset.sdf, there seem to be more than the 3 columns required for running the process. So I tried some versions with the extra columns deleted. No matter what I do, I get an error after entering the following command:

cxtrain pka -i mypka PB.sdf

I have added cxtrain to environmental variables, ensured that I have an updated, 32-bit Java, and the sdf file is located in the MarvinBeans folder (which I navigate to before calling the command).

The error I am seeing is: ZIP file must have at least one entry

at Source)

at  Source)

at Source)

at chemaxon.calculations.pka.PKaTraining.zipAllParamterFiles(

at chemaxon.calculations.PKaTraining.calculatepKaIncrements(

at chemaxon.marvin.Trainer.main(

Note: Parameter is spelled wrong in the error, that was not a typo on my part.

Most of the time it makes a file (located in Users\username\chemaxon, not in Program Files) which shows as a PKADATA file that is 0 kb.

If someone could help me, it's been giving me major headaches! Thank you!


ChemAxon d51151248d

06-01-2016 10:45:23

Hi Casey, 

First sorry for the delayed response. We have been out of office due to the holidays recently. 

About the bug: in order to fix it we should have the file that caused the error. Can you attach in your next response the modified file that caused the bug? 

Thank you,