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H3 modeling takes 10 days more?

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H3 modeling takes 10 days more?

Hi: I runned Rosetta for H3_modeling 10 days ago use linux computer.

now I check the folder H3_modeling. the 10 models still in progress.

anyone know when it will finish.


Thanks a lot


Post Situation: 
Fri, 2017-10-27 03:11

Since I don't know much about your simulation environment, can you share your input files? Also, are the jobs still running, and if so, can you share a log file?

Fri, 2017-10-27 08:30

The job is still running.

Thanks here is the command I used: ( I did from model 0 to model 9)

$ROSETTA_BIN/antibody_H3.linuxclangrelease \
@abH3.flags \
-s grafting/model-0.relaxed.pdb \
-nstruct 1000 \
-antibody:auto_generate_kink_constraint \-antibody:all_atom_mode_kink_constraint \
-multiple_processes_writing_to_one_directory \
-out:file:scorefile H3_modeling_scores.fasc \
-out:path:pdb H3_modeling > h3_modeling-0.log 2>&1 &

Please see attached for input and log file.

Thanks so much. Now it has been 2 weeks

Mon, 2017-10-30 18:29


Can I continue to do other task on Rossetta without finshing H3 modeling task?


Mon, 2017-10-30 18:52

You can certainly do other tasks in the meantime; this job consumes a single CPU. If you have more than one core in your machine, or available to you on a cluster, you can do whatever else you like.

You unfortuanately haven't provided the flags file that you used, abH3.flags.

Mon, 2017-10-30 21:45

Here is the contain of abH3.flags, any problem with this?

Thanks so much!

$ less abH3.flags

-antibody::refine               refine_kic
-antibody::cter_insert          false
-antibody::flank_residue_min    true
-antibody::bad_nter             false
-antibody::h3_filter            false
-antibody::h3_filter_tolerance  5

#more standard settings, for packages used by antibody_H3
-extrachi_cutoff 0

#these are standard settings for kic/ngk
-loops:legacy_kic false
-loops:kic_min_after_repack true
-loops:allow_omega_move true    ### remove 'true' and loop::?
-kic_bump_overlap_factor 0.36
-loops:refine_outer_cycles 5


Wed, 2017-11-01 01:50

OK, when I try to run with those flags it tells me that I don't have fragment files; by default it's looking for a file called frag9. Are there fragment files or flags that you haven't provided yet? You could try sending me your *exact* run directory as a zipped file so this doesn't happen again.

Wed, 2017-11-01 10:49


I am unable to upload zip file. here is the link for the file.

Thanks a lot

Fri, 2017-11-03 20:15