pepspec anchor dock

[Anonymous]

What am I doing wrong?

Here is the call command:

/Users/andreserobian/Documents/rosetta/main/source/bin/./pepspec_anchor_dock.macosclangrelease -in:file:s her2+ile_ABC.pdb -out:pdb 1

Here is the output:

core.init: Checking for fconfig files in pwd and ./rosetta/flags 

core.init: Rosetta version: rosetta.binary.mac.release-247 r247 2020.08+release.cb1cabafd74 cb1cabafd7463ab703f6abf5efa33d2707b85924 https://www.rosettacommons.org 2020-02-22T06:57:31.821199

core.init: command: /Users/andreserobian/Documents/rosetta/main/source/bin/./pepspec_anchor_dock.macosclangrelease -in:file:s her2+ile_ABC.pdb -out:pdb 1

basic.random.init_random_generator: ‘RNG device’ seed mode, using ‘/dev/urandom’, seed=512937896 seed_offset=0 real_seed=512937896

basic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=512937896 RG_type=mt19937

core.init: Resolved executable path: /Users/andreserobian/Documents/rosetta/main/source/bin/./pepspec_anchor_dock.macosclangrelease

core.init: Looking for database based on location of executable: /Users/andreserobian/Documents/rosetta/main/database/

ERROR: Value of inactive option accessed: -out:file:o

 

[Anonymous]

Ok, it seems I have the correct -out:file:o, now the ref_pdb_list file is called but fails to read the pdb file, any thoughts?

Here is the call command:

/Users/andreserobian/Documents/rosetta/main/source/bin/./pepspec_anchor_dock.macosclangrelease -pepspec:ref_pdb_list pep_ref -out:file:o h1

Here is the output:

core.init: Checking for fconfig files in pwd and ./rosetta/flags 

core.init: Rosetta version: rosetta.binary.mac.release-247 r247 2020.08+release.cb1cabafd74 cb1cabafd7463ab703f6abf5efa33d2707b85924 https://www.rosettacommons.org 2020-02-22T06:57:31.821199

core.init: command: /Users/andreserobian/Documents/rosetta/main/source/bin/./pepspec_anchor_dock.macosclangrelease -pepspec:ref_pdb_list pep_ref -out:file:o h1

basic.random.init_random_generator: ‘RNG device’ seed mode, using ‘/dev/urandom’, seed=-153857200 seed_offset=0 real_seed=-153857200

basic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=-153857200 RG_type=mt19937

core.init: Resolved executable path: /Users/andreserobian/Documents/rosetta/main/source/bin/./pepspec_anchor_dock.macosclangrelease

core.init: Looking for database based on location of executable: /Users/andreserobian/Documents/rosetta/main/database/

ERROR: no ref pdbs loaded!

ERROR:: Exit from: src/apps/public/pepspec/pepspec_anchor_dock.cc line: 500

[ ERROR ]: Caught exception:

File: src/apps/public/pepspec/pepspec_anchor_dock.cc:500

[ ERROR ] UtilityExitException

ERROR: no ref pdbs loaded!

AN INTERNAL ERROR HAS OCCURED. PLEASE SEE THE CONTENTS OF ROSETTA_CRASH.log FOR DETAIL

I have made a pdb ref file accroding to <homolog_pdb_filename> <peptide_chain> <peptide_anchor_res> (seperated by TAB spaces) named ‘pep_ref’ that reads:

name1.pdb <TAB> C <TAB> 1

 

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