error using ward or jarp

Hi,

I have a compound lib with ~5000 structures in an sdf created with InstantJChem.

Generation of a CF descriptor using generatemd was done:

• generatemd c library.sdf -k CF -f 512 -o generatemd_f512_2.txt

If I now start the jarp or ward procedure in order to cluster the structures:

• jarp -i generatemd_f512.txt -f 512 -t 0.1 -c 0.3 -o OUT

and the following error appears (HEAP_LIMIT is 1024):

Error: For input string: "chemaxon.descriptors.ChemicalFingerprint"

 

Can anyone please help me.Thanks alot in advance,

manni

Hi Manni,

The default output format of generatemd does not directly fit to the required input format of jarp and ward. Modifiers need to be used in the command line of generatemd to ensure that the output is written in the proper format. These flags are -D and -g in this case.

You may wish to take a look at the explanation of these command line options, and also see some examples.

Hope this helps,

Regards

Miklos