H3 modeling takes 10 days more?

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    • October 27, 2017 at 10:11 am #2761
      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

      • October 27, 2017 at 3:30 pm #13831
        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?

        • October 31, 2017 at 1:29 am #13840
          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

          • October 31, 2017 at 1:52 am #13841
            Anonymous

               

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

               

            • October 31, 2017 at 4:45 am #13843
              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.

              • November 1, 2017 at 8:50 am #13848
                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)

                   

                • November 1, 2017 at 5:49 pm #13854
                  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.

                  • November 4, 2017 at 3:15 am #13861
                    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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