Can’t generate a cst file to use with ddg_monomer application

[Anonymous]

Hi everyone,

I would like to create some double mutations in my protein and thought to get a prediction of the ddG change using Rosetta’s ddg_monomer application. I tried running the preminimization using:

/usr/local/bin/Rosetta/rosetta_bin_linux_2019.40.60963_bundle/main/source/bin/minimize_with_cst.linuxgccrelease -in:file:l lst -in:file:fullatom -ignore_unrecognized_res -fa_max_dis 9.0 -database /usr/local/bin/Rosetta/rosetta_bin_linux_2019.40.60963_bundle/main/database/ -ddg::harmonic_ca_tether 0.5 -ddg::constraint_weight 1.0 -ddg::out_pdb_prefix min_cst_0.5 -ddg::sc_min_only false > mincst.log

and I get a mincst.log back containing:

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

core.init: Rosetta version: rosetta.binary.linux.release-234 r234 2019.40+release.513cc22 513cc22d17d203e95eda08f3e66a985d92be7bfe https://www.rosettacommons.org 2019-10-05T17:00:56.548952

core.init: command: /usr/local/bin/Rosetta/rosetta_bin_linux_2019.40.60963_bundle/main/source/bin/minimize_with_cst.linuxgccrelease -in:file:l lst -in:file:fullatom -ignore_unrecognized_res -fa_max_dis 9.0 -database /usr/local/bin/Rosetta/rosetta_bin_linux_2019.40.60963_bundle/main/database/ -ddg::harmonic_ca_tether 0.5 -ddg::constraint_weight 1.0 -ddg::out_pdb_prefix min_cst_0.5 -ddg::sc_min_only false

basic.random.init_random_generator: ‘RNG device’ seed mode, using ‘/dev/urandom’, seed=12883808 seed_offset=0 real_seed=12883808

basic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=12883808 RG_type=mt19937

core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set.  Created 980 residue types

core.chemical.GlobalResidueTypeSet: Total time to initialize 3.97531 seconds.

core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015

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 = 9)

core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 9)

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: Database file opened: scoring/score_functions/rama/fd/all.ramaProb

basic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb

basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt

basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt

basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt

basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt

basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA

basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n

core.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated.

basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop

apps.public.ddg.minimize_with_cst: using -l option

And when I try to run the convert_to_cst_file.sh to get my constraints file I get a file with:

AtomPair CA  CA  HARMONIC 

with no constraints. The convert script reads:

#!/bin/tcsh

# This is a script to convert the contents of a log file generated by

# pre-relaxing the crystal structure of the wild-type species with

# the minimize_with_cst application into a set of Calpha distance

# restraints for use in the ddg_monomer application.  The script reads

# from a file and sends its output to standard-out.

#

# The first argument to this script should be the name of the log file.

# Its output should be redirected to text file.

# e.g.:

# ./convert_to_cst_file.sh cstmin.log > ca_dist_restraints.cst

grep ^apps.public.ddg.minimize_with_cst: $1 | awk ‘{print “AtomPair CA “$7” CA “$9” HARMONIC “$11” “$14}’

I guess the script picked up the last line in mincst.log and then had nothing to go on(?)

Any ideas to repair this would be greatly appreciated.

Have a good weekend!,

Chi

[Anonymous]

Is that your whole log file? I think maybe the log file should end with a line indicating success e.g. `protocols.jd2.JobDistributor: 1 jobs considered, 1 jobs attempted in n seconds` . That log file looks like it was cut off in the middle. Sometimes there are buffering issues with log writing that result in partial logs. If what you’ve pasted there is the whole log file you have on disk, it’s missing the piece the script is trying to parse. The script is looking for some lines with structural coordinates.

[Anonymous]

Hi,

Thanks for the reply. 

That is the whole of the log file so I guess whatever its done I haven’t any co-ordinates to run the convert after(?) Not sure where to go from there as I’m just trying to run the tutorial from 

https://new.rosettacommons.org/docs/latest/application_documentation/analysis/ddg-monomer

at the moment using the tutorial files so was hoping those would be error free.

Has anyone else run the tutorial and come across the same problem?

Thanks!,

Chi

[Anonymous]

Can you try running `/usr/local/bin/Rosetta/rosetta_bin_linux_2019.40.60963_bundle/main/source/bin/minimize_with_cst.linuxgccrelease -in:file:l lst -in:file:fullatom -ignore_unrecognized_res -fa_max_dis 9.0 -database /usr/local/bin/Rosetta/rosetta_bin_linux_2019.40.60963_bundle/main/database/ -ddg::harmonic_ca_tether 0.5 -ddg::constraint_weight 1.0 -ddg::out_pdb_prefix min_cst_0.5 -ddg::sc_min_only false` (remove the `> mincst.log` portion) and see if that produces a complete log? Please report here what comes out.

It will just show up on the terminal so you’ll have to copy/paste from terminal to mincst.log. 

[Anonymous]

Hi,

So I ran the commands without the ‘>mincst.log’ and the terminal returned:

/home/oem/Documents/rosetta_bin_linux_2019.40.60963_bundle/main/source/bin/minimize_with_cst.linuxgccrelease -in:file:l lst -in:file:fullatom -ignore_unrecognized_res -fa_max_dis 9.0 -database /home/oem/Documents/rosetta_bin_linux_2019.40.60963_bundle/main/database/ -ddg::harmonic_ca_tether 0.5 -ddg::constraint_weight 1.0 -ddg::out_pdb_prefix min_cst_0.5 -ddg::sc_min_only false

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

core.init: Rosetta version: rosetta.binary.linux.release-234 r234 2019.40+release.513cc22 513cc22d17d203e95eda08f3e66a985d92be7bfe https://www.rosettacommons.org 2019-10-05T17:00:56.548952

core.init: command: /home/oem/Documents/rosetta_bin_linux_2019.40.60963_bundle/main/source/bin/minimize_with_cst.linuxgccrelease -in:file:l lst -in:file:fullatom -ignore_unrecognized_res -fa_max_dis 9.0 -database /home/oem/Documents/rosetta_bin_linux_2019.40.60963_bundle/main/database/ -ddg::harmonic_ca_tether 0.5 -ddg::constraint_weight 1.0 -ddg::out_pdb_prefix min_cst_0.5 -ddg::sc_min_only false

basic.random.init_random_generator: ‘RNG device’ seed mode, using ‘/dev/urandom’, seed=603907263 seed_offset=0 real_seed=603907263

basic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=603907263 RG_type=mt19937

core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set.  Created 980 residue types

core.chemical.GlobalResidueTypeSet: Total time to initialize 1.70045 seconds.

core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015

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 = 9)

core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 9)

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: Database file opened: scoring/score_functions/rama/fd/all.ramaProb

basic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb

basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt

basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt

basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt

basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt

basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA

basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n

core.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated.

basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop

apps.public.ddg.minimize_with_cst: using -l option

Best,

Chi

[Anonymous]

I think the ddg monomer tutorial is out of date. Try this instead. (Note the author who wrote the ddg-monomer documentation in 2015 is an author on the flex-ddg documents in 2018)

https://pubmed.ncbi.nlm.nih.gov/29401388/

https://github.com/Kortemme-Lab/flex_ddG_tutorial

[Anonymous]

Hi,

That’s a shame – it was a simple tutorial for a novice (like me…) 

Thanks for the link – will give it a go and see how far I get! 

Kind regards,

Chi

[Author]

Posts