I am working with Pradeep who posted below. I thought I would add some screenshots to layout an specific example in the hope that some useful feedback can be received.

In this example, DGEBA and 3,3'-Sulfonyldianiline are attempting to be cross-linked. I have included the two structures below for clarity. Note that the Name field has been changed to indicate the epoxide and primary amine sites.

The third figure indicates the inputs to the Pipeline Pilot protocol "Create Polymer Network". In the input I have specified that for Reaction 1, the two reactants are the epoxide and the primary amine sites. The reaction type has been specified as Ring Opening as the epoxide ring should be broken as a consequence of the reaction.

The fourth and final figure shows the reactant results of the running of the protocol. As can been seen in the figure, there has been absolutely no cross-linking achieved. I am at a loss as to why this is the case as the older cross-linking Perl script from this site (which has less apparent capability) works fine with similar input. The script runs without error to the end and I can see that the expected number of molecular dynamics runs are being carried out.

Does anyone have an idea of what is being done incorrectly here? Advice on how to achieve cross-linking using the Create Polymer Network protocol would be gratefully received.