User 8a7878ec6d

09-05-2014 11:42:19


I'm trying to calculate BCUT descriptors on an SD file  (JChem 6.2.2, Windows 7) using the following command:

generatemd c input.sdf -k BCUT -c config.xml -o output.txt

The config .xml file looks like this, taken straight from your web site:

<BCUT Type="Charge" Lowest="1" Highest="1" />
<BCUT Type="Polarizability" Lowest="1" Highest="1" />
<BCUT Type="HBond" Lowest="1" Highest="1" />

If I run the command, nothing happens, I just get 'Check configuration fil config.xml'.

Please advice.

Kind regards,


ChemAxon 5fc3e8d7d0

09-05-2014 15:38:36


An example BCUT descriptor configuration is available in your JCHEM directory (examples/config/bcut.xml) or use the following link:
http://www.chemaxon.com/jchem/examples/config/bcut.xml />
See the attached config file with your settings.

Best regards,

User 8a7878ec6d

13-05-2014 13:10:27

Hi again,

It works with this bcut-example.xml file, sort of, but I first get an error message:

Too many arguments after -k, ignored

The calculation runs to its end, and 4 BCUT values rather than 6 are calculated for each compound.

Regards, Evert

ChemAxon d51151248d

06-06-2014 11:06:28

Hi evehom, 

Sorry for the late answer. The behaviour of the BCUT calculation you reported is a real issue, and we are investigating it further.

We will come back to you soon with a solution.

Best regards,


ChemAxon 5fc3e8d7d0

13-06-2014 08:12:42


We have fixed this issue. The fix will be available in the next major release.

Best regards,