I have a system consisting of a protein with 3 chains, ATP, 2 RNA strands, Mg, Zn and a ligand. For the ATP and RNA names of the residues are A T, U P and G P which I change them to RA T, RU P and RG P to be read by AMBER FF. Each of the parts (protein, ATP and RNAs) seems to be working fine separatrly for making topology, however, when I strip out the ligand and ions from the pdb structure and try to make a topology of the protein, ATP and RNA, it stops with an error complaining that ‘atom P in residue RG 0 was not found in rtp entry RG5’. Charmm FF can not make the topology either saying ‘atom N is not found in ACE1’, though I dont have any N in my structure for ACE and I checked the merged.rtp and there is no N in the ACE either. I also tried to consider each part as a ligand to make a topology with a server but it failed. Can this system be simulated at all, since it is complicated and if yes, how can I solve this problem?