I am trying to calculate rmsd using a template pdb structure using score_jd2. When I try to run the following command,
$ROSETTA3/bin/score_jd2.macosclangrelease -in:file:silent decoys_alp_tcn.out -evaluation:rmsd 2alp.pdb `cat pdb_list` FULL -out:file:silent rescored_decoys.out
it errors out saying ERROR: Unrecognized residue: SO4. Then I rerun the same with
Then I get the following error:
ERROR: [ERROR] Error opening RBSeg file 'batch_000065_000059'
What does this mean? How should I fix it?
You have the format for -evaluation:rmsd a bit off. (Don't worry - it's a relatively common issue.) Key to understanding the format is that the intent is to allow you to do multiple rmsd calculations to different (sub)-structures all at the same time.
The -evaluation:rmsd option takes triples of values. (More or less - there are some options which can extend the number of entries.) So in a well formatted -evaluation:rmsd you'll have a multiple of three entries after it, and each set of three will be taken as a group.)
The first entry is the reference structure - this is the structure you're comparing to.
The second is the label you'll use in the scorefile to identify this particular RMSD calculation. (So if you have multiple reference structures you can label each of them differently.)
The third and last entry is the specification of what sub-structure you're interested in calculating the rmsd over. This can either be the literal string "FULL" to specify using the rmsd to the complete structure, or it can be a filename to a RBSeg file which specifies the residues over which to calculate the rmsd.
So I'm guessing that you have more than one structure in your pdb_list file, which means that Rosetta is reading the first entry as the column label, and then reads the second one ('batch_000065_000059') as the RBSeg file which specifies the subset of residues to use. It therefore tries to open it, and fails, resulting in the error message.
What you probably want to do is something like `$ROSETTA3/bin/score_jd2.macosclangrelease -in:file:silent decoys_alp_tcn.out -evaluation:rmsd 2alp.pdb to_2alp FULL -out:file:silent rescored_decoys.out`
By the way, you want to be careful with `-ignore_unrecognized_res` with referece structures for RMSD calculations. In most cases Rosetta matches up residues for RMSD calculations in a very simple 1:1 manner. If there are a different number of residues in the reference structure, or they're in a different order, then the RMSD calculation will either crash or give bad results. I'd recommend pre-processing the reference PDB structure and then checking that the number and order of residues matches up with what you expect.