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Thanks smslewis and rmorreti for your help and getting me that far already. I already had a look at the thread you mentioned above yesterday after rmorreti’s reply.
I am facing a problem though, as in my case I am trying to generate a params file for the chromophore in GFP (1EMA.pdb) and the carbonyl carbon and the “alpha carbon” are not linked but in between there is C-N-C so the “backbone” looks like this N-C-C-N-C-C(O). I noted in the readme file in the tarball with the code to generate a polymer type residue this line: “Note: You will need to add some additional code to work with your additional backbone atom.” I have no idea where to start.
Also the chromophore doesn’t have a “sidechain” but there are several “sidechains coming out of the backbone” which I anticipate will be another problem I will run into.
I would very much appreciate your help