Hard coded limits in qprep and qatom

[acmnpv]

Currently there are a number of hard coded limits in both the qatom and the qprep module. Those concern the maximum number of atoms in the FEP file and the maximum number of atoms in a residue. Even though those limits are violated, Q will happily build a topology and try to run it with no chance of succeeding.
This should be changed to either

• fail the topology building / run initialisation with warning to the user
  or
• replacing of hard coded limits by dynamic memory allocation

This issue is just for me as a reminder to fix this.