Atom names containing ' cannot be used

[PabloNA97]

In adaptive, the templetized pele control file is read and and saved in a different file after substituting the required fields. The new pele control file is saved using the makeWorkingControlFile() function in line 215 of simulation/simulationrunner.py. By default, makeWorkingControlFile substitutes all ' characters in the string by ", see line 231 of simulation/simulationrunner.py. Perhaps there was a good reason to do this, but it's a problem when trying to use as ANM nodes atoms that contain the ' character in their name. This is the case for example in RNA molecules using the AMBER99sbBSC0 which is implemented in PELE (e.g. H5'', C5', C2').

Thus one cannot include the following configuration:

"algorithm": "CARTESIANS", "nodes": { "atoms": { "names": ["P_", "C2", "_C4'"]}}

Because it's transformed into:

"algorithm": "CARTESIANS", "nodes": { "atoms": { "names": ["P_", "C2", "_C4""]}}

Which is not a properly formed json control file (additional ")

Thanks :)