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error: Unable to open weights/patch file in using ddg_monomer.linuxgccrelease

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error: Unable to open weights/patch file in using ddg_monomer.linuxgccrelease
#1

 

 

Dear Friends and experts

I am trying to use "ddg_monomer.linuxgccrelease". First I want to pre-minimize the structure and get mincst.log file. I put all options in a flag file called pre_minimize

I run the following command:

/home/jy/rosetta3.10/rosetta_bin_linux_2018.33.60351_bundle/main/source/bin/minimize_with_cst.linuxgccrelease @pre_minimize

1. To pre-minimize, the command from protocol is as following:

/path/to/minimize_with_cst.linuxgccrelease -in:file:l lst -in:file:fullatom -ignore_unrecognized_res -fa_max_dis 9.0 -database /path/to/rosetta_database/ -ddg::harmonic_ca_tether 0.5 -score:weights standard -ddg::constraint_weight 1.0 -ddg::out_pdb_prefix min_cst_0.5 -ddg::sc_min_only false -score:patch rosetta_database/scoring/weights/score12.wts_patch > mincst.log

the content of pre_minimize flag file is what follows

-in:file:s adtppvg_10.pdb
-in:file:fullatom
-ignore_unrecognized_res
-fa_max_dis 9.0
-database /home/jy/rosetta3.10/rosetta_bin_linux_2018.33.60351_bundle/main/database
-ddg::harmonic_ca_tether 0.5
-score:weights pre_talaris_2013_standard
-restore_pre_talaris_2013_behavior
-ddg::constraint_weight 1.0
-ddg::out_pdb_prefix min_cst_0.5
-ddg::sc_min_only false
-score:patch score12.wts_patch > mincst.log

I changed -score:wights standard to score12, ref2015 and re_talaris_2013_standard, respectively. Then I run the command, all of which returned me same error message as follows:

ERROR: Unable to open weights/patch file. None of (./)> or (./)>.wts_patch or /home/jy/rosetta3.10/rosetta_bin_linux_2018.33.60351_bundle/main/database/scoring/weights/> or /home/jy/rosetta3.10/rosetta_bin_linux_2018.33.60351_bundle/main/database/scoring/weights/>.wts_patch exist
ERROR:: Exit from: src/core/scoring/ScoreFunction.cc line: 2749

I aslo tried copy weights files to current working directory  or specify the full path to weights file which is /home/jinyan/rosetta3.10/rosetta_bin_linux_2018.33.60351_bundle/main/database/scoring/weights/pre_talaris_2013_standard. But I still get same error message. I do not know how to ssolve this problem and I am wondering whether you could please help me out. I would be much appreciated.

Thanks again

Best regards

xinmiao

 

 

Post Situation: 
Thu, 2020-01-30 22:09
xinmiaohe

Hi, dear friends and experts

I am new to rosetta so I meet a lot problem while running applications. Now I meet some problems I really do not know how to solve. I am wondering whether someone could lease help me out. I would be much appreciated.

I modified my command a little bit and, it report me another error. I do not know how to fix this so I am wondering whether someone can help me out. Thank you very very very much!!!

/home/jinyan/rosetta3.10/rosetta_bin_linux_2018.33.60351_bundle/main/source/bin/minimize_with_cst.linuxgccrelease -in:file:s adtppvg_10.pdb -out:level 500 @pre_minimize > mincst.log

this is error message in my mincst.log file

using -s option
examining file: ATOM
core.import_pose.import_pose: [ ERROR ] File: ATOM not found!
caught exception

File: src/core/import_pose/import_pose.cc:336
[ ERROR ] UtilityExitException
ERROR: Cannot open file "ATOM"

I also attched my pdb file.

The following is flag file of preminimize

-in:file:fullatom
-ignore_unrecognized_res
-fa_max_dis 9.0
-database /home/jinyan/rosetta3.10/rosetta_bin_linux_2018.33.60351_bundle/main/database
-ddg::harmonic_ca_tether 0.5
-score:weights pre_talaris_2013_standard
-restore_pre_talaris_2013_behavior
-ddg::constraint_weight 1.0
-ddg::out_pdb_prefix min_cst_0.5
-ddg::sc_min_only false
-score:patch score12.wts_patch
-out:level 500

File attachments: 
Fri, 2020-01-31 08:23
xinmiaohe