openmm molcrys to openmm conversion bug

[RagnarB83]

Introduced a bug at some point in openmm-basic-test.py and MD-cluster-openMMMD.py that converts from ASH forcefield file to OpenMM xml file:
openmmobject = OpenMMTheory(cluster_fragment=Cluster, ASH_FF_file=ff_file, platform='CPU')

Error message:

Traceback (most recent call last):
  File "/Users/bjornsson/ownCloud/ASH-tests/testsuite/openmm-basic-test.py", line 12, in <module>
    openmmobject = OpenMMTheory(cluster_fragment=Cluster, ASH_FF_file=ff_file, platform='CPU')
  File "/Users/bjornsson/ASH/ash-dev/ash/interfaces/interface_OpenMM.py", line 549, in __init__
    self.system = self.forcefield.createSystem(self.topology, nonbondedMethod=openmm.app.NoCutoff,
  File "/Users/bjornsson/miniconda/envs/ASHnewv1/lib/python3.9/site-packages/openmm/app/forcefield.py", line 1206, in createSystem
    templateForResidue = self._matchAllResiduesToTemplates(data, topology, residueTemplates, ignoreExternalBonds)
  File "/Users/bjornsson/miniconda/envs/ASHnewv1/lib/python3.9/site-packages/openmm/app/forcefield.py", line 1420, in _matchAllResiduesToTemplates
    raise ValueError('No template found for residue %d (%s).  %s' % (res.index+1, res.name, _findMatchErrors(self, res)))
ValueError: No template found for residue 1 (RS0).  This might mean your input topology is missing some atoms or bonds, or possibly that you are using the wrong force field.

At least a bug present in the PDB-file that is created:

ATOM  1     R00  RS0      1     -2.630  -1.841   0.331  1.00  0.00      SEG B
ATOM  2     R01  RS0      1     -1.902   2.488   0.331  1.00  0.00      SEG B
ATOM  3     R02  RS0      1     -2.630  -2.488  -4.036  1.00  0.00      SEG B
ATOM  4     R03  RS0      1     -1.902   1.841  -4.036  1.00  0.00      SEG B
ATOM  5     R04  RS0      1      2.630   1.841  -0.331  1.00  0.00      SEG B
ATOM  6     R05  RS0      1      1.902  -2.488  -0.331  1.00  0.00      SEG B
ATOM  7     R06  RS0      1      2.630   2.488   4.036  1.00  0.00      SEG B
ATOM  8     R00  RS0      2      1.902  -1.841   4.036  1.00  0.00      SEG B
ATOM  9     R01  RS0      2     -4.031  -0.210   2.062  1.00  0.00      SEG C

Probably related