# H3 modeling takes 10 days more?

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H3 modeling takes 10 days more?
#1

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

Jessica

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

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
everyday847

The job is still running.

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

$ROSETTA_BIN/antibody_H3.linuxclangrelease \ @abH3.flags \ -s grafting/model-0.relaxed.pdb \ -nstruct 1000 \ -antibody:auto_generate_kink_constraint \-antibody:all_atom_mode_kink_constraint \ -multiple_processes_writing_to_one_directory \ -out:file:scorefile H3_modeling_scores.fasc \ -out:path:pdb H3_modeling > h3_modeling-0.log 2>&1 & Please see attached for input and log file. Thanks so much. Now it has been 2 weeks File attachments: Mon, 2017-10-30 18:29 jessye Can I continue to do other task on Rossetta without finshing H3 modeling task? Mon, 2017-10-30 18:52 jessye You can certainly do other tasks in the meantime; this job consumes a single CPU. If you have more than one core in your machine, or available to you on a cluster, you can do whatever else you like. You unfortuanately haven't provided the flags file that you used, abH3.flags. Mon, 2017-10-30 21:45 everyday847 Here is the contain of abH3.flags, any problem with this? Thanks so much!$ less abH3.flags

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

#more standard settings, for packages used by antibody_H3
-ex1
-ex2
-extrachi_cutoff 0

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

(END)

Wed, 2017-11-01 01:50
jessye

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
everyday847

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

Thanks a lot

Fri, 2017-11-03 20:15
jessye