Hi all,
I tried clustering decoy pdbs from a docking run using the following command
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/opt/rosetta/rosetta_source/bin/cluster.linuxgccrelease -database /opt/rosetta/rosetta_database -in:file:l ./list-of-pdbs.txt -nooutput > cluster.log3
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It seems to read the files. Below is the very end of the log file
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protocols.jobdist.main: Starting complexppk_moveddecoy_56890_0001 ...
core.conformation.Conformation: Found disulfide between residues 23 93
core.conformation.Conformation: Found disulfide between residues 135 209
core.conformation.Conformation: Found disulfide between residues 257 299
core.conformation.Conformation: Found disulfide between residues 338 382
core.pack.task: Packer task: initialize from command line()
RESCORING!
protocols.jobdist.main: Finished complexppk_moveddecoy_56890_0001 in 1 seconds.
protocols.jobdist.JobDistributors: Looking for an available job: 1 49 49
protocols.jobdist.main: Starting _0001 ...
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But in the shell I get the following error
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ERROR: !pdb.empty()
ERROR:: Exit from: src/core/io/pdb/pdb_dynamic_reader.cc line: 208
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Can someone please tell me what's wrong or if I'm missing anything please.
(However when I do a cluster test with the following command it seems to work!
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/opt/rosetta/rosetta_source/bin/cluster.linuxgccrelease -database /opt/rosetta/rosetta_database -in:file:s ./complexppk_moveddecoy_01231.pdb ./complexppk_moveddecoy_05035.pdb ./complexppk_moveddecoy_06937.pdb ./complexppk_moveddecoy_07736.pdb -out:prefix cluster -nooutput > cluster.log2
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I'm trying to avoid giving the names of 50 files that's in my list to the above command! So any help is appreciated)
Thanks.
My guess is that one of the files listed in ./list-of-pdbs.txt doesn't contain any usable atom coordinates. Check if you have any non-pdb files listed, or any empty files, or even if you have a valid PDB file, but with all zero values in the occupancy field. (By default, Rosetta discards any atoms which are listed with zero occupancy values. A quick test is to add the flag -run:trust_missing_coords to the command line, which will cause Rosetta to trust the coordinates given for zero occupancy atoms.)