Automated manufacturing systems (AMSs) use a limited set of resources to process multiple parts simultaneously. Inappropriate resource allocation may lead to deadlocks in AMSs. Deadlocks can cause some parts to never be finished, resulting in enormous economic losses. To this end, this work extends the existing models of resource-oriented Petri nets (ROPNs) to establish special resource marked graphs (SRMGs). In contrast to existing deadlock prevention strategies, A-structures are proposed to represent a special kind of deadlock caused by the inability to complete assembly operations. To simplify the structure of the supervisor, the subset of saturable structures is found based on the inclusion and coverage relation. By designing controllers for each structure in this subset and central hazard structures, the supervisor for the entire system is obtained. It can prevent SRMGs from reaching unsafe markings. Then, resource buffer subnets are added for SRMGs to resolve blocking issues. This can ensure that parts requiring failed resources will not affect the normal production of other parts. Eventually, an example is given to illustrate the application prospect and performance of the method.