FlexPepDocking with GDP-bound protein

[Anonymous]

I have a problem when doing the FlexPepDocking to a receptor with GDP bound, but it stop with an error, saying that GDP is an unrecognized residue. When I add a flag “-remember_unrecognized_res”, it goes well but GDP was still missing in the output structure. I believe GDP is involved in the binding and I don’t want to ingore it in the docking. And I check the database, GDP.params is in /rosetta_database/chemical/residue_type_sets/fa_standard/residue_types/nucleic. However, after I search in this forum, I found that another topic said that “Having a GTP molecule present durng docking is not possible in the current version of RosettaDock”. So I am wondering whether the new version of RosettaDock supports this function. If it supports, is this error just caused by the name of the atoms in my pdb file. Attached is the coordinate file of my GDP.
Thank you in advance.
Gary

[Anonymous]

By default, while GDP is present in the database, it’s not loaded. Take a look at /rosetta_database/chemical/residue_type_sets/fa_standard/residue_types.txt and you’ll notice that the line for GDP.params is commented out. Remove the “#” from the front of the line, and Rosetta should now be able to recognize GDP residues.

That does not mean, however, that FlexPepDocking will then work appropriately. I’m not familiar with FlexPepDocking specifically, but unfortunately working in the presence of ligands is often an afterthought in Rosetta development, so there may be some assumptions in the protocol which means it won’t work. I’d recommend trying it, though, and see what sort of results/errors you get.

[Anonymous]

Thank you rmoretti. After removing the “#” and changing the names of all atoms according to the standard GDP.params. Now the program recognizes GDP. However, an error “segmentation fault” happens when I put it in the same chain of the receptor numbered after the C terminal. When I put it in a single chain different from the peptide and the receptor, another error “ERROR: unknown atom_name: GDP CA”. Any idea?
Thanks again.

Now it works, after putting the GDP as a single chain following the peptide chain.

[Anonymous]

Generally, when preparing a PDB file for use in Rosetta, you want to use a separate chain for each different (covalent) molecule. Ideally, though, the program should give you a better diagnostic message, rather than segfaulting.

Usually when I see something like “unknown atom_name: … CA” it’s because Rosetta is trying to calculate C-alpha RMSD statistics from the structure. Since the ligand doesn’t have a alpha carbon, it triggers the message. If it’s just an informative RMSD calculation, the “error” message shouldn’t be too big a deal – it will calculate the RMSD to the residues it can and continue on. If the program is halting after the error message, however, it’s some other issue.

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