Knowledge Base

Article ID: 
1 930
- Last Modified: August 11, 2015 - 12:00am

When running the hydrogen bond assignment stage of the Protein Preparation Wizard, I get an error in the log file that PROPKA failed for my structure: WARNING: PropKa failed on this structure - disabling use of PropKa. Is there a fix for this problem?

This is likely be due to a file permission problem, which occurs on Linux machines. To fix it, change the permissions on the file $HOME/.python-eggs, by entering the following command in a terminal window:

chmod 755 $HOME/.python-eggs

You should then be able to run the protein preparation job successfully.

You might also have to change the ownership of this directory, if it is owned by root. To do this you must have superuser privilege.

sudo chown username $HOME/.python-eggs

To ask a question or get help, please submit a support ticket or email us at help@schrodinger.com.

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