- This topic has 24 replies, 3 voices, and was last updated 13 years, 8 months ago by
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First, part A) The NC resfile tag is not meant to interact with metal ions. The packer should (?) ignore metal ions, as it knows they have no rotamers. At most you need a NATRO flag for the calcium positions.
First, part
Is it failing at PDB read-in, or at resfile read-in? Do you have a calcium residue type? It will be at something like rosetta_database/chemical/residue_type_sets/fa_standard/residues/(metals?). There should be several ions in that folder; if there isn’t a calcium you can make one by comparison.Second: I’m not sure what you’re asking. Do you mean, how do you specify which residues interact with the calcium? There isn’t really a way to do that; Rosetta’s energy function doesn’t handle that sort of bond. Usually we place the metal ion where we want it and fix the rotamers interacting with it (using NATRO).
Third: If you want your spin-label group to be present in the modeling, you will need to generate a parameters file for it, as you suggest. It will probably be easiest to generate a whole residue (including the cysteine backbone) rather than just the added atoms. You can do this by generating a .mol file (pymol can do it) of just your modified residue and feeding it to the molfile_to_params.py package in Rosetta. Partial charges, etc, are largely irrelevant: score12 (the default scorefunction) ignores them. If you want to use charges, you can tweak the scorefunction to use one of the explicit electronic terms (rather than fa_pair), but I don’t know how to do it.
Third, part
: If you want this new cysteine conjugate to be flexible, it is possible, but it is nontrivial. I’ve done it in the past with help from its author. I don’t think the code for generating rotamer libraries for non-canonical residue types has been released yet; I’ll ask its author. -
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A) You can save log files by redirecting the output (this is supported in most shells): backrub.linuxgccrelease -option1 -option2 > logfile. The > redirects output to logfile.
Can you attach your resfile and params file?C) Does your input PDB contain a residue of the adduct type, or a regular cysteine? You can try it both ways. If you name it like the adduct, then the PDB reader should be able to add the extra adduct atoms, even if you give it cysteine as input (be sure to remove HG).
D) It does not matter what folder the new parameters file is in, so long as the path is accurate – the folders themselves are only for organization. It does matter that you put it in the fa_standard residue type set.
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I can spot three issues:
A) core.pack.rotamer_set.RotamerSet_: [ WARNING ] including current in order to get at least 1 rotamer !!!!!! 60 cym
This means you have not provided any rotamers for your new residue – I thought you said you were going to make your own rotamer library? I notice there’s no PDB_ROTAMERS line in the params file. core.mm.MMBondAngleLibrary: No parameters for X-X-C
This is a combination of two problems. The direct problem is that your MMBondAngleLibrary does not have bond angle parameters for that bond. The reason it doesn’t have them is that two of the atoms have MM atom types of “X”. To fix this, you’ll need to edit your params file so that the fourth column in the atom definition lines is a valid MM atom type. The MM atom types are in chemical/mm_atom_type_sets/fa_standard/mm_atom_types; I think they’re from CHARMM, hopefully those files will make it clear. If your ligand has new atom types, you’ll need to add them to the files in that directory and find parameters for them that are consistent with the same forcefield (again, I think it’s CHARMM).C) “and in the PDB file there was actually e.g C01 C03 C05.. instead of e.g CZ CT1 CT2 in the params file. ” I don’t understand the question – if you don’t like the atom names in the INPUT pdb, then you should change them to match the params file. Is this in relation to an output pdb…?
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