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MSMS troubleshooting

resolve issues with the MSMS installation

Issue 1: RunError: ... 'Broken pipe'

If the msms test case (python fails with the following error:

msms test ... Loading PDB...
Getting surfaces via the MSMS executable
executing: /home/biskit/py/biskit/external/msms//gpdb_to_xyzrn
in folder: /home/biskit/py/biskit/external/msms/
RunError: Couldn't run or communicate with external program: 'Broken pipe'

this usually means that the gawk program is not installed. Test run the gpdb_to_xyzrn script:


Which will in this case result in:

biskit/external/msms//gpdb_to_xyzrn: 102: gawk: not found


Install the gawk program, for example on Ubuntu:

sudo apt-get install gawk