Flexpep docking freezing issue at “press enter to continue”

[Anonymous]

Hi all,

I searched on the forum and couldn’t find this so I hope it isn’t a repeat. I’m trying to dock using flexpepdocking.linuxgcc.release. I have tried this from the command line but I have been recently have been trying to run it from a script that looks like this:

the issue is whether I run it from the command line or the script the program will not continue. this is what my screen looks like:

./../../bin/FlexPepDocking.graphics.linuxgccrelease -s ac4_1-cav_combine-first_motif.pdb -database ../../../rosetta_database -flexpep_prepack -ex1 -ex2aro -unboundrot 2011-caveolin-3.pdb;
./../../bin/FlexPepDocking.graphics.linuxgccrelease -s ac3_1-cav_combine-first_motif.pdb -database ../../../rosetta_database -out:file:silent decoys.silent -out:file:silent_struct_type binary -pep_refine -use_input_sc -ex1 -ex2aro -nstruct 100 -unboundrot 2011-caveolin-3.pdb -lowres_preoptimize;

and this is my run:

/ac3_models/flexpep$ ./script_demo
core.init: Mini-Rosetta version Unversioned directory from unknown
core.init: command: ./../../bin/FlexPepDocking.graphics.linuxgccrelease -s ac3_1-cav_combine-first_motif.pdb -database ../../../rosetta_database -flexpep_prepack -ex1 -ex2aro -unboundrot 2011-caveolin-3.pdb
core.init: ‘RNG device’ seed mode, using ‘/dev/urandom’, seed=-168505198 seed_offset=0 real_seed=-168505198
core.init.random: RandomGenerator:init: Normal mode, seed=-168505198 RG_type=mt19937
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: standard
core.scoring.ScoreFunctionFactory: SCOREFUNCTION PATCH: score12
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.
basic.io.database: Database file opened: scoring/score_functions/PairEPotential/pdb_pair_stats_fine
basic.io.database: Database file opened: scoring/score_functions/hbonds/standard_params/HBPoly1D.csv
basic.io.database: Database file opened: scoring/score_functions/hbonds/standard_params/HBFadeIntervals.csv
basic.io.database: Database file opened: scoring/score_functions/hbonds/standard_params/HBEval.csv
basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/env_log.txt
basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cbeta_den.txt
basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/pair_log.txt
basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cenpack_log.txt
basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/env_log.txt
basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cbeta_den.txt
basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/pair_log.txt
basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cenpack_log.txt
basic.io.database: Database file opened: scoring/score_functions/MembranePotential/CEN6_mem_env_log.txt
basic.io.database: Database file opened: scoring/score_functions/MembranePotential/CEN10_mem_env_log.txt
basic.io.database: Database file opened: scoring/score_functions/MembranePotential/memcbeta_den.txt
basic.io.database: Database file opened: scoring/score_functions/MembranePotential/mem_pair_log.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
basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_pp
basic.io.database: Database file opened: scoring/score_functions/rama/Rama_smooth_dyn.dat_ss_6.4
basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/env_log.txt
basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cbeta_den.txt
basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/pair_log.txt
basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cenpack_log.txt
core.pack.rotamer_set.UnboundRotamersOperation: Adding ‘unbound’ rotamers from 2011-caveolin-3.pdb
core.chemical.ResidueTypeSet: Finished initializing fa_standard residue type set. Created 6225 residue types
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: standard
core.scoring.ScoreFunctionFactory: SCOREFUNCTION PATCH: score12
protocols.jd2.PDBJobInputter: Instantiate PDBJobInputter
protocols.jd2.PDBJobInputter: PDBJobInputter::fill_jobs
protocols.jd2.PDBJobInputter: pushing ac3_1-cav_combine-first_motif.pdb nstruct index 1
protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active …
protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job
core.pack.task: Packer task: initialize from command line()
protocols.jd2.PDBJobInputter: filling pose from PDB ac3_1-cav_combine-first_motif.pdb
FlexPepDockingProtocol: apply
FlexPepDockingProtocol: WARNING: No native supplied by used – using starting structure as reference for statistics
protocols.flexPepDocking.FlexPepDockingFlags: Receptor chain: A
protocols.flexPepDocking.FlexPepDockingFlags: Receptor first res: 1
protocols.flexPepDocking.FlexPepDockingFlags: Receptor nres: 151
protocols.flexPepDocking.FlexPepDockingFlags: Peptide chain: B
protocols.flexPepDocking.FlexPepDockingFlags: Peptide first res: 152
protocols.flexPepDocking.FlexPepDockingFlags: Peptide nres: 80
protocols.flexPepDocking.FlexPepDockingFlags: Peptide anchor: 168
protocols.flexPepDocking.FlexPepDockingFlags: # peptide anchors: 1
protocols.flexPepDocking.FlexPepDockingFlags: # peptide cuts: 0
protocols.flexPepDocking.FlexPepDockingFlags: Receptor anchor: 66
core.pack.task: Packer task: initialize from command line()
core.pack.rotamer_set.UnboundRotamersOperation: Adding ‘unbound’ rotamers from 2011-caveolin-3.pdb
core.pack.dunbrack: Dunbrack library took 0.04 seconds to load from binary
Press enter to continue…

After hitting enter nothing happens, in order for me to get a response I have to hit ctrl+c to force quit. As you can see my script runs this program twice, one for prepacking and one for the actuall run (almost identical to the manual tips/example section) and I get the staling on both runs. Did I forget a flag? hopefully this is just a simple fix and won’t take up too much of anyone’s time.

Thanks for the help,
Ryan

[Anonymous]

You are trying to run in graphics mode (FlexPepDocking.GRAPHICS.linuxgccrelease). The “Press enter to continue” bit has to do with the graphics system. I’ve never used the graphics, but I assume that’s where the error is from this evidence. Compile without graphics and see if it runs (using FlexPepDocking.default.linuxgccrelease, or FlexPepDocking.linuxgccrelease).

If you really mean to be using graphics, we can try to debug that, but let’s check that the nongraphics version is working first.

[Anonymous]

Thank you it seems to be working, sorry took me so long to respond I had to rebuild rosetta to run without graphics.

Ryan

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