Issue 1: RunError: ... 'Broken pipe'
If the msms test case (python msms.py) fails with the following error:
msms test ... Loading PDB... Getting surfaces via the MSMS executable Running 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