atom P in the residue RG 0 was not found in rtp entry RG5

Hi all,

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?

Thank you.

With something with as many components as that, it is better to generate the topology for one molecule at a time. So generate a coordinate file which contains only one molecule, then pass that to pdb2gmx and work through the errors if/as they appear. Dealing with one molecule at a time is much easier.

Then you can convert each of the .top files you generated into a .itp and simply included then within the .top. Personally I find it much easier to work with a short .top that then points to separate .itp files for each of the type of molecules.