Hey, I was testing the enzyme design application with the files (1a91_CHGW_d1_mod.pdb, D2N_aX.params, D2N_ax_confs.pdb, Est_CHba_d2n.cst and flags) provided in one of the test folders.
Here is my command line:
/usr/local/rosetta3.2/rosetta_source/bin/enzyme_design.linuxgccrelease -database /usr/local/rosetta3.2/rosetta_database/ -overwrite @flags > enzyme_design.log
The run stopped a few seconds after it started. Here is the short log file:
core.init: Mini-Rosetta version exported from unknown
core.init: command: /usr/local/rosetta3.2/rosetta_source/bin/enzyme_design.linuxgccrelease -database /usr/local/rosetta3.2/rosetta_database/ @flags
core.init: 'RNG device' seed mode, using '/dev/urandom', seed=1505122273 seed_offset=0 real_seed=1505122273
core.init.random: RandomGenerator:init: Normal mode, seed=1505122273 RG_type=mt19937
core.scoring.etable: Starting energy table calculation
core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well
core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)
core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)
core.scoring.etable: Finished calculating energy tables.
core.io.database: Database file opened: /usr/local/rosetta3.2/rosetta_database/pdb_pair_stats_fine
core.io.database: Database file opened: /usr/local/rosetta3.2/rosetta_database/scoring/score_functions/hbonds/standard_params/HBPoly1D.csv
core.io.database: Database file opened: /usr/local/rosetta3.2/rosetta_database/scoring/score_functions/hbonds/standard_params/HBFadeIntervals.csv
core.io.database: Database file opened: /usr/local/rosetta3.2/rosetta_database/scoring/score_functions/hbonds/standard_params/HBEval.csv
core.io.database: Database file opened: /usr/local/rosetta3.2/rosetta_database/P_AA
core.io.database: Database file opened: /usr/local/rosetta3.2/rosetta_database/P_AA_n
core.io.database: Database file opened: /usr/local/rosetta3.2/rosetta_database/P_AA_pp
core.io.database: Database file opened: /usr/local/rosetta3.2/rosetta_database/Rama_smooth_dyn.dat_ss_6.4
core.scoring.etable: Using alternate parameters: LJ_RADIUS_SOFT in Etable construction.
core.scoring.etable: Starting energy table calculation
core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well
core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)
core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)
core.scoring.etable: Finished calculating energy tables.
apps.public.enzdes.enzyme_design: Finished all 0 structures in 2 seconds.
Warning: No structures processed. Existing output files may have been skipped, did you mean to delete them or to use the -overwrite flag?
Based on the first line, is the failure caused by the lack of Minirosetta_database?
Thanks a lot for the help!
"Warning: No structures processed. Existing output files may have been skipped, did you mean to delete them or to use the -overwrite flag?"
This almost certainly means you already had done the run once and thus had the results already in the directory (probably named ????_0001.pdb, or with a 0001 tag in a silent file). (It may ship with a copy of the results already present.). Either deleting the pre-existing result, or using -overwrite, should fix this.
That was what I thought, but I don't see any new files (other than enzyme.design.log) generated in the folder. Sometimes I also got an error message like this:
[root@localhost test]# /usr/local/rosetta3.2/rosetta_source/bin/enzyme_design.linuxgccrelease -database /usr/local/rosetta3.2/rosetta_database/ @flags > enzyme_design.log
ERROR: Cannot find file 'inputs/D2N_aX.params'
ERROR:: Exit from: src/core/chemical/residue_io.cc line: 139
But the D2N_aX.params file is right there in the folder...I'm buffled now.
That sounds like you are having file system permission problems. If the file system is refusing Rosetta access, it will fail to find inputs/D2N_aX.params, and it will fail to know if the ??_0001.pdb file already exists (leading to the -overwrite warning).
Are you running from within the Rosetta source you installed? Try copying out the demo folder to a separate location, checking the permissions, and running from there.
I am somewhat concerned that you are running as root; Rosetta doesn't require it (although installing to /usr/local might). I always have 10 copies of Rosetta anyway so I've never tried installing in that fashion.
Hi many thanks for helping me out..
I checked on the file permissions..they seem to be fine. Besides, I had no trouble running protein design, ligand and protein docking previously, with the modified files copied from the demos folders..
Here is how I usually run things:
/usr/local/rosetta3.2/rosetta_source/bin/enzyme_design.linuxgccrelease -database /usr/local/rosetta3.2/rosetta_database/ @flags > enzdes.log
The input, flags, params and cst files are all in the folder /usr/local/rosetta3.2/my_file/....
I will try it again by shifting files around after my finals. Thanks for the help!
I assume you're running the test provided in the test/integration/tests/enzdes directory. (The path you provided got cut off.)
What you probably want to do is copy that entire directory as-is to a convenient location. Then you would change directories into that copied directory, and while in that directory, run your "/usr/local/rosetta3.2/rosetta_source/bin/enzyme_design.linuxgccrelease -database /usr/local/rosetta3.2/rosetta_database/ @flags > enzdes.log"
Note that there is an "inputs" subdirectory. You want to keep it as a subdirectory, as the flags file, as written, specifies a relative path to the files (if you look at the flags file you'll see the "inputs/..." designation of files. -- Note that you can put all the files into a single directory, but you'll have to change the flags file to refer to the correct location.
Silly me, thought I had changed the flags file. Thanks, that solves my problem.