# Can only relax one structure at a time

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Can only relax one structure at a time
#1
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:
Wed, 2012-12-12 01:55
lah435

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?

Wed, 2012-12-12 06:49
smlewis

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.

Wed, 2012-12-12 11:06
rmoretti

"How do I convert between Unix and Windows text files?"

http://kb.iu.edu/data/acux.html

Fri, 2012-12-14 13:40
smlewis