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?