H3 modeling takes 10 days more?

[Anonymous]

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

[Anonymous]

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?

[Anonymous]

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

[Anonymous]

 

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

 

[Anonymous]

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.

[Anonymous]

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

-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)

 

[Anonymous]

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.

[Anonymous]

 

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

Thanks a lot

https://www.dropbox.com/s/wu5rnhhexuj24c6/1a2y.tar.gz?dl=0

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