Reply To: Ab Initio Modelling of Protein with Small-Molecule Cofactor

[Anonymous]

It was really the identifier for the ligand, as rmoretti suggested. After adding “Z” before [FAD] in the fasta input no more errors occurred and I now get structures with a correct coordination of the FAD.

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So, in summary for anyone who wants to do something similar, here is the way it works:

1) convert a pdb file of your ligand to a param file using the /[..]/rosetta_source/src/python/apps/public/molfile_to_params.py python script WITH “-c option” to create centroid and full atom parameter files
2) add the unique identifiers from your .params file to your fasta sequence (you may want to change NAME and IO_STRING of your ligand in the .params file)
3) adjust your constraint files and the “.residue_pair_jump_cst” accordingly (pay special attention to different atom nomenclature)
4) feed your ligand .params files to rosetta using the “-extra_res_cen” and “-extra_res_fa” flags

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Thank you all so much for your helpful suggestions. I really appreciate your advise.