ERROR: Unused “free” argument specified: GDP.fa.tors

Ok, here’s my full script. It’s funny now I’m getting a different error below.

#!/bin/bash



$ROSETTA3/source/bin/rosetta_scripts.linuxgccrelease 

    -in::file: /home/labusr/Documents/starting_single_dimer.pdb 

    -parser::protocol /home/labusr/Documents/asymm_refine.xml 

    -parser::script_vars denswt=35 rms=1.5 reso=4.4 map=TetraAllPF_8nm_half1_b250_f4_4A_corr.mrc testmap=TetraAllPF_8nm_half2_b250_f4_4A_corr.mrc

    -ignore_unrecognized_res 

    -edensity::mapreso 4.4 

    -default_max_cycles 200 

    -edensity::cryoem_scatterers 

    -beta 

    -out::suffix _$1

    -crystal_refine

    -extra_res_cen GTP.cen.params GDP.cen.params 

    -extra_res_fa GTP.fa.params GDP.fa.params

    -extra_improper_file GTP.fa.tors GDP.fa.tors

core.init: Rosetta version rosetta.source.release-152:d6547f6858282e67c41356255dfdd63b0e7a75aa 2017-09-08 02:01:37.594540 from http://www.rosettacommons.org

core.init: command: /home/labusr/rosetta/main//source/bin/rosetta_scripts.linuxgccrelease -in::file: /home/labusr/Documents/starting_single_dimer.pdb -parser::protocol /home/labusr/Documents/asymm_refine.xml -parser::script_vars denswt=35 rms=1.5 reso=4.4 map=TetraAllPF_8nm_half1_b250_f4_4A_corr.mrc testmap=TetraAllPF_8nm_half2_b250_f4_4A_corr.mrc -ignore_unrecognized_res -edensity::mapreso 4.4 -default_max_cycles 200 -edensity::cryoem_scatterers -beta -out::suffix _ -crystal_refine

core.init: 'RNG device' seed mode, using '/dev/urandom', seed=1470792057 seed_offset=0 real_seed=1470792057

core.init.random: RandomGenerator:init: Normal mode, seed=1470792057 RG_type=mt19937

core.init: Resolved executable path: /home/labusr/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/rosetta_scripts.default.linuxgccrelease

core.init: Looking for database based on location of executable: /home/labusr/rosetta/main/database/

protocols.jd2.PDBJobInputter: Instantiate PDBJobInputter

protocols.jd2.PDBJobInputter: PDBJobInputter::fill_jobs

protocols.jd2.PDBJobInputter: pushed /home/labusr/Documents/starting_single_dimer.pdb nstruct index 1

protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ...

protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job

protocols.jd2.PDBJobInputter: filling pose from PDB /home/labusr/Documents/starting_single_dimer.pdb

core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set.  Created 557 residue types

core.chemical.GlobalResidueTypeSet: Total time to initialize 0.52 seconds.

core.import_pose.import_pose: [ ERROR ] File: /home/labusr/Documents/starting_single_dimer.pdb not found!



ERROR: Cannot open file "/home/labusr/Documents/starting_single_dimer.pdb"

ERROR:: Exit from: src/core/import_pose/import_pose.cc line: 324

BACKTRACE:

/home/labusr/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libutility.so(utility::exit(std::string const&, int, std::string const&, int)+0x27f) [0x7f9a741e948f]

/home/labusr/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libcore.5.so(core::import_pose::pose_from_file(core::pose::Pose&, core::chemical::ResidueTypeSet const&, std::string const&, core::import_pose::ImportPoseOptions const&, bool, core::import_pose::FileType)+0x389) [0x7f9a7868b1c9]

/home/labusr/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libcore.5.so(core::import_pose::pose_from_file(core::pose::Pose&, std::string const&, core::import_pose::ImportPoseOptions const&, bool, core::import_pose::FileType)+0x50) [0x7f9a7868c330]

/home/labusr/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libcore.5.so(core::import_pose::pose_from_file(core::pose::Pose&, std::string const&, bool, core::import_pose::FileType)+0x3b) [0x7f9a7868c51b]

/home/labusr/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libprotocols.1.so(protocols::jd2::PDBJobInputter::pose_from_job(core::pose::Pose&, std::shared_ptr<protocols::jd2::Job>)+0x3d5) [0x7f9a790cdd75]

/home/labusr/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libprotocols.1.so(protocols::jd2::JobDistributor::run_one_job(std::shared_ptr<protocols::moves::Mover>&, long, std::string&, std::string&, unsigned long&, unsigned long&, bool)+0x6aa) [0x7f9a790a805a]

/home/labusr/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libprotocols.1.so(protocols::jd2::JobDistributor::go_main(std::shared_ptr<protocols::moves::Mover>)+0xc1) [0x7f9a790a9f71]

/home/labusr/rosetta/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libprotocols.1.so(protocols::jd2::FileSystemJobDistributor::go(std::shared_ptr<protocols::moves::Mover>)+0x4a) [0x7f9a790816ba]

/home/labusr/rosetta/main//source/bin/rosetta_scripts.linuxgccrelease() [0x403408]

/lib64/libc.so.6(__libc_start_main+0xf5) [0x7f9a721dec05]

/home/labusr/rosetta/main//source/bin/rosetta_scripts.linuxgccrelease() [0x403d4b]

Error: [ ERROR ] ERROR: Exception caught by JobDistributor while trying to get pose from job 'starting_single_dimer__0001'

Error: [ ERROR ]



[ ERROR ] EXCN_utility_exit has been thrown from: src/core/import_pose/import_pose.cc line: 324

ERROR: Cannot open file "/home/labusr/Documents/starting_single_dimer.pdb"





Error: [ ERROR ] Treating failure as bad input; canceling similar jobs

protocols.jd2.FileSystemJobDistributor: job failed, reporting bad input; other jobs of same input will be canceled: starting_single_dimer__0001

protocols.jd2.JobDistributor: no more batches to process...

protocols.jd2.JobDistributor: 1 jobs considered, 1 jobs attempted in 0 seconds

Error: [ ERROR ] Exception caught by rosetta_scripts application:1 jobs failed; check output for error messages

Error: [ ERROR ]

./A_asymm_refine.sh: line 14: -extra_res_cen: command not found

./A_asymm_refine.sh: line 15: -extra_res_fa: command not found

./A_asymm_refine.sh: line 16: -extra_improper_file: command not found

First, I want to debug the bash script, becasuse it doesn’t seem to be working! It initially runs fine, then gives these errors ./”name of script”.sh: line 14: “flag”: command not found. I attached the script, it’s better to inspect it to verify the syntax is correct. Thanks a lot, I appreciate your help.

Fantastic, now after fixing that stuff (sorry I’m familiar with python more than bash), I get the same error as in the python script (which makes more sense):

[labusr@luxor nucleotide_refienment]$ ./A_asymm_refine.sh

ERROR: ERROR: Unused "free" argument specified: GDP.fa.tors

Error: [ ERROR ] Exception caught by rosetta_scripts application:ERROR: ERROR: Unused "free" argument specified: GDP.fa.tors

Error: [ ERROR ]

[labusr@luxor nucleotide_refienment]$

Edit:

I contacted Frank, he told me to cat the two files. Thanks a lot for all of your help.