- This topic has 3 replies, 3 voices, and was last updated 10 years, 11 months ago by Anonymous.
December 12, 2012 at 9:55 am #1485Anonymous
I have never been able to give the relax application more than one structure at a time, but now I have hundreds and doing each individually just isn’t an option. How can I do this?
my flags file contains:
the inputs file contains:
all the input files are in the current directory.
The error is:
protocols.jd2.PDBJobInputter: pushing 00_wildtype_0016_0201.pdb nstruct index 1
protocols.jd2.PDBJobInputter: pushing 00_wildtype_0016_0202.pdb nstruct index 1
protocols.jd2.PDBJobInputter: pushing 00_wildtype_0016_0203.pdb nstruct index 1
core.io.pdb.file_data: Adding undetected upper terminus type! 146
core.pack.task: Packer task: initialize from command line()
protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ...
core.import_pose.import_pose: PDB File:00_wildtype_0016_0001.pdb not found!
Note that if I specify a single structure in the flags file:
It works just fine.
How is it possible to give Rosetta a list of structures to work on?
December 12, 2012 at 2:49 pm #8226Anonymous
This ought to work fine, assuming that 00_wildtype_0016_0001.pdb is in the directory in which you are running Rosetta (which it would have to be for -s 00_wildtype_0016_0001.pdb to work without a path).
Post your -l file. My best guess is there is some sort of nonprinting character at the end of the line in your -l file. Are you using any path options in your options file?
December 12, 2012 at 7:06 pm #8228Anonymous
The non-printing charachter is my guess too. That would be especially likely if you prepared the list with a Windows machine (which ends lines with a ‘rn’ combo) and were reading it on a Linux or MacOS 10 machine (which end lines with just ‘n’). The “extra” ‘r’ may be confusing things.
December 14, 2012 at 9:40 pm #8236Anonymous
“How do I convert between Unix and Windows text files?”
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