Currently there were problems regarding running simulations of a protein without a ligand, mainly:

• The script expected smallMoleculeForcefield in several parts, which was not present while creating a simulation with only the protein in place.
• The postprocessing was also adjusted to expect a ligand

Changes made:

• Fixing of openmmdl_analysis.py script generation for protein only simulations
• Adjustment of post_md_conversion.py to be compatible with protein only simulations

PR Checklist

• Issue raised/referenced?
• Tests updated/added?
• Documentation updated/added?
• CHANGELOG file updated?
• Is your name in AUTHORS?