Thank you, Alessandra, for your reply. I have a confusion here that when I merge the topology I will have to reindex ligand atoms. *e.g *I have ligand topology starting with atom number 1 and bond terms, angles, dihedrals have all the connectivity numbering from 1 to so on. When I will change the index number in combined topology; will it not affect these terms? Could you please explain a bit more? I have attached a ligand file for reference. Thanks in advance.
Sadaf
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