BioNetGen allows intramolecular bonds between components on the same species and correctly handles input/output of species containing them. NFsim also seems to correctly simulate species with intramolecular bonds but the .species file generated from a configuration that has intramolecular bonds can be incorrect, as the attached example demonstrates. In this model there is a species M(a!1,b!1) that incorrectly gets written to the .species file as M(a!1,b!2).
intramolbond.bngl.txt
BioNetGen allows intramolecular bonds between components on the same species and correctly handles input/output of species containing them. NFsim also seems to correctly simulate species with intramolecular bonds but the .species file generated from a configuration that has intramolecular bonds can be incorrect, as the attached example demonstrates. In this model there is a species
M(a!1,b!1)that incorrectly gets written to the .species file asM(a!1,b!2). intramolbond.bngl.txt