Dear Rosetta Support,
I am trying to create a homology model of the tubulin protein heterodimer. I want to include the GTP/magnesium and GDP/magnesium (which are in the crystal structure template I am using) in the modelling process, but I am having problems. I keep getting an error that says either the scoring function "is not setup for nonideal/cartesian scoring", or that my residue param file, e.g. GTP.fa.tors "does not have valid atom records" (or something along those lines).
I have attached the relevant files. Because I can't upload more than 3 files, the GTP related files are all merged into one file. If you search for the appropriate file name (as indicated by the command file, i.e. GTP.fa.params, GTP.fa.tors, GTP.cen.params) within "GTPparams_and_TemplatePDB.txt" you will be directed to the text within those respective files. My template also has GDP, but the files for those are directly analogous to the GTP files. Also, the PDB section of templ_thread.pdb is merged with the file showing my command line input (i.e. the attached file, command_and_nucleotidePDBs.txt).
I can see how my GTP.fa.tors file is a problem, since all the torsions values are the same. However, I can't seem to generate a valid torsions file using the molfile_to_params command. I am also aware that GTP is in the residues.txt file from the source code, but I tried activating those (by uncommting them in the residues.txt file) and I simply get the previously mentioned error message about my scoring function. In any case, I am wondering whether it's valid to use the default GDP and GTP parameters anyway, since they're clearly not optimized for modeling the tubulin protein.
I should also note that I ignored the non-standard residues (i.e. the nucleotides) when I threaded my sequence onto my template. I then manually inserted the nucleotide section of the original PDB (which, like I mentioned, is shown in the file "command_and_nucleotidePDBs.txt") into templ_thread.pdb. I realize this means that there are no weights for the nucleotides in templ_thread.pdb, and the sequence at the beginning of templ_thread.pdb does not include the nucleotide residue codes (I suppose these could be contributing to my problems, but I don't know a valid solution!).
Any help resolving these issues would be much appreciated!
|xml input file||1.01 KB|
|command line input, and the nucleotide section of templ_thread.pdb||7.44 KB|
|relevant GTP parameter files||12.58 KB|