cluster error

[Anonymous]

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.

[Anonymous]

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.)

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