# RIFdocking：Unable to locate database file chemical/residue_type_sets/fa_standard/residue_types/

3 posts / 0 new
RIFdocking：Unable to locate database file chemical/residue_type_sets/fa_standard/residue_types/
#1

Hello, everyone, I encountered some problems when I was doing Step 19: Actual motif grafting of RIFdocking.
First, I need to turn my scaffolding into a silent files. The command is as follows:

cat scaffolds.list | silentfrompdbsparallel > scaffolds.silent

After the command is run, I got the following error:

-rw-rw-r-- 1 dengxj dengxj 74616 8月   3 10:38 scaffolds.list
(python3.9) [dengxj@node01 New Folder]$cat scaffolds.list | silentfrompdbs > scaffolds.silent PyRosetta-4 2022 [Rosetta PyRosetta4.Debug.python39.linux 2022.28+release.6c2ddeccd31e780da01b0cbbf3e33949218c99d9 2022-07-12T15:12:13] retrieved from: http://www.pyrosetta.org (C) Copyright Rosetta Commons Member Institutions. Created in JHU by Sergey Lyskov and PyRosetta Team. core.init: Checking for fconfig files in pwd and ./rosetta/flags core.init: Rosetta version: PyRosetta4.Debug.python39.linux r324 2022.28+release.6c2ddec 6c2ddeccd31e780da01b0cbbf3e33949218c99d9 http://www.pyrosetta.org 2022-07-12T15:12:13 core.init: command: PyRosetta -l tmp_19kt58E52hatf.list -out:file:silent tmp_i6SwNld3fdmPI.silent -out:file:silent_struct_type binary -extra_res_fa /home/bcov/from/jason/H3i.am1bcc.fa.mm.params -database /opt/software/anaconda3/envs/python3.9/lib/python3.9/site-packages/pyrosetta-2022.28+release.6c2ddec-py3.9-linux-x86_64.egg/pyrosetta/database basic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=-682888727 seed_offset=0 real_seed=-682888727 basic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=-682888727 RG_type=mt19937 protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ... protocols.jd2.PDBJobInputter: Instantiate PDBJobInputter protocols.jd2.PDBJobInputter: PDBJobInputter::fill_jobs protocols.jd2.PDBJobInputter: pushed /home/dengxj/RIFdock/supplemental_files/scaffolds/HHH_bc/HHH_bc_16171.pdb nstruct index 1 ...... ...... ...... core.scoring.etable: Finished calculating energy tables. basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv basic.io.database: [ WARNING ] Unable to locate database file chemical/residue_type_sets/fa_standard/residue_types//home/bcov/from/jason/H3i.am1bcc.fa.mm.params ERROR: Cannot find file '/home/bcov/from/jason/H3i.am1bcc.fa.mm.params or /opt/software/anaconda3/envs/python3.9/lib/python3.9/site-packages/pyrosetta-2022.28+release.6c2ddec-py3.9-linux-x86_64.egg/pyrosetta/database/chemical/residue_type_sets/fa_standard/residue_types//home/bcov/from/jason/H3i.am1bcc.fa.mm.params' ERROR:: Exit from: /home/benchmark/rosetta/source/src/core/chemical/residue_io.cc line: 143 Traceback (most recent call last): File "/home/dengxj/RIFdock/supplemental_files/cao_2021_protocol/github_backup/silent_tools/pyjd2", line 18, in <module> JobDistributor.get_instance().go( protocols.simple_moves.ScoreMover() ); RuntimeError: File: /home/benchmark/rosetta/source/src/core/chemical/residue_io.cc:143 [ ERROR ] UtilityExitException ERROR: Cannot find file '/home/bcov/from/jason/H3i.am1bcc.fa.mm.params or /opt/software/anaconda3/envs/python3.9/lib/python3.9/site-packages/pyrosetta-2022.28+release.6c2ddec-py3.9-linux-x86_64.egg/pyrosetta/database/chemical/residue_type_sets/fa_standard/residue_types//home/bcov/from/jason/H3i.am1bcc.fa.mm.params' silent_tools: Error! Silent file doesn't exist: tmp_i6SwNld3fdmPI.silent silent_tools: Error! Silent file doesn't exist: tmp_i6SwNld3fdmPI.silent rm: cannot remove"tmp_i6SwNld3fdmPI.silent": No such file or directory rm: cannot remove"tmp_i6SwNld3fdmPI.silent.idx": No such file or directory (python3.9) [dengxj@node01 New Folder]$ 

And the ‘silentfrompdbsparallel’ in the command line has been uploaded.

I found some similar problems in Rosetta Commons, and the solutions provided did not solve my problem. So can someone give me some advice? Thank you very much.

AttachmentSize
1011 bytes
Category:
Post Situation:
Tue, 2022-08-02 20:06
sia

It looks like the issue is not the silentfrompdbsparallel script, but rather the silentfrompdbs script it uses.

There's a reference to H3i.am1bcc.fa.mm.params somewhere in that script, and while it might have worked on the machine of the person who wrote it, it's not working on your machine.

I doubt you need that params file, so you can probably just delete the -extra_res_fa /home/bcov/from/jason/H3i.am1bcc.fa.mm.params entry that's probably somewhere in that script.

Wed, 2022-08-03 08:34
rmoretti

You can fix this error by revise the script of "silentfrompdbs" file as upper user commented.

Open "silentfrompdbs" file and find the command line below.

$jd2_program -l$tmp_list -out:file:silent $tmp_file -out:file:silent_struct_type binary -extra_res_fa /home/bcov/from/jason/H3i.am1bcc.fa.mm.params 1>&2 Then delete the flag "-extra_res_fa /home/bcov/from/jason/H3i.am1bcc.fa.mm.params" from the line. Change like this:$jd2_program -l $tmp_list -out:file:silent$tmp_file -out:file:silent_struct_type binary 1>&2

If you save the changes and run it, you can normally use the program.

Mon, 2022-08-15 18:31
SeongRyeong Go