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:
-in:file:l inputs
the inputs file contains:
00_wildtype_0016_0001.pdb
00_wildtype_0016_0002.pdb
...
00_wildtype_0016_0203.pdb
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 ...
protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job
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:
-in:file:s 00_wildtype_0016_0001.pdb
It works just fine.
How is it possible to give Rosetta a list of structures to work on?
Post Situation:
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?
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 '\r\n' 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.
"How do I convert between Unix and Windows text files?"
http://kb.iu.edu/data/acux.html