Hi, How is it possible that you have finished up to production run without the .top file ? The first line of your ebolaag.top says that the topology has been generated. How have you been doing any of the equilibration steps without the .top file? Information regarding atoms are there in the ebolaag_Protein_chain_A.itp and the ebolaag_Ion_chain_A2.itp files created by pdb2gmx. Your comments do not make any sense to me.
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