Help with enzyme design

[Anonymous]

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!

[Anonymous]

“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.

[Anonymous]

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.

[Anonymous]

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.

[Anonymous]

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!

[Anonymous]

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.

[Anonymous]

Silly me, thought I had changed the flags file. Thanks, that solves my problem.

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