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Unrecognised resiudues when rescoring PDB files generated by enzyme_design under MPI

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Unrecognised resiudues when rescoring PDB files generated by enzyme_design under MPI
#1

Hello,

I'm running the enzyme_design application using MPI and in the scorefile that is produced, the 'description' field isn't unique across the processors, so if I run on 10 processors, I get 10 PDB files named mypdb___DE_10.pdb. Firstly, is there a way to ensure that the PDB files have unique names?

As I can't correlate the scores in the scorefile to the individual PDB file, I've renamed all my PDB files to give them unique names and am then trying to use the score_jd2 to generate a scorefile. I'm using the following flags:

/opt/rosetta_bin_linux_2017.08.59291_bundle/main/source/bin/score_jd2.default.macosclangrelease \
-database /opt/rosetta_bin_linux_2017.08.59291_bundle/main/database \
-in:file:l pdb.list \
-out:file:o rescorefile.json \
-scorefile_format json \
-extra_res ../SAM.params \
-extra_res ../SAX.params \
-ignore_unrecognized_res \

However this generates the following error:

protocols.jd2.PDBJobInputter: pushed 1m6e_scaffold__DE_98.pdb nstruct index 1
protocols.jd2.PDBJobInputter: pushed 1m6e_scaffold__DE_99.pdb nstruct index 1
protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ...
protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job
protocols.jd2.PDBJobInputter: filling pose from PDB 1m6e_scaffold__DE_1.pdb
core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set.  Created 546 residue types
core.chemical.GlobalResidueTypeSet: Total time to initialize 0.820689 seconds.
core.import_pose.import_pose: File '1m6e_scaffold__DE_1.pdb' automatically determined to be of type PDB
core.chemical.ResidueTypeFinder: No ResidueTypes remain after filtering by ResidueType base name: 'SAX'

ERROR: No match found for unrecognized residue at position 1
Looking for lower-terminal residue with 3-letter code: MET
ERROR:: Exit from: src/core/io/pose_from_sfr/PoseFromSFRBuilder.cc line: 433

So it's firstly falling over on the MET residue, even though I'm passing the -ignore_unrecognized_res  flag, and also looks like it's not reading the information on the ligands that I'm passing with the -extra_res flag.

Rosetta must be able to score these PDB file as it generated them with a scorefile, so can anyone tell me what I need to do to recreate the scorefile?

Thanks!

Jens

 

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Post Situation: 
Tue, 2018-02-13 03:41
linucks