Merge pull request #314 from marrink-lab/feature/command-limit

Limit the line length for the command in the top

bin/martinize2

@@ -686,9 +686,17 @@ def entry():
  LOGGER.debug("Writing molecule {}.", molecule, type='step')
 
  # Write the topology if requested
+ # grompp has a limit in the number of character it can read per line
+ # (due to the size limit of a buffer somewhere in its implementation).
+ # The command line can be longer than this limit and therefore
+ # prevent grompp from reading the topology.
+ gromacs_char_limit = 4000 # the limit is actually 4095, but I play safe
+ command = ' '.join(sys.argv)
+ if len(command) > gromacs_char_limit:
+ command = command[:gromacs_char_limit] + ' ...'
  header = [
  'This file was generated using the following command:',
- ' '.join(sys.argv),
+ command,
  VERSION,
  ]
  if None not in ss_sequence: