Regarding snugdock Ag-Ab score

Member Site › Forums › ROSIE › ROSIE – General › Regarding snugdock Ag-Ab score

Viewing 4 reply threads
  • Author
    Posts
    • December 10, 2018 at 10:47 pm #3052
      Anonymous

        Hi There,

        I am running snugdock locally for an Ag-Ab complex.  Program is running fine but I am getting all score value 0.00.

        SCORE: total_score         rms CAPRI_rank       Fnat       I_sc       Irms   Irms_leg atom_pair_constraint                cbeta              cen_rms chainbreak complex_normalized           dG_cross dG_cross/dSASAx100 dG_separated dG_separated/dSASAx100 dSASA_hphobic dSASA

        SCORE:       0.000       4.622      1.000      0.250     -9.228      3.186      2.599                0.000              169.078                2.973      1.684              0.662              0.000              0.000       -2.243                 -0.203       557.632  1105SCORE:       0.000       5.659      1.000      0.370    -14.032      2.651      2.143                0.000              168.115                5.569      1.478              0.687              0.000              0.000       35.761                  1.931       832.898  1851

        SCORE:       0.000       4.820      1.000      0.272    -19.858      3.393      3.089                0.000              168.160                4.229      1.468              0.775              0.000              0.000       -8.163                 -0.533       731.121  1532SCORE:       0.000       6.191      1.000      0.217    -10.966      3.229      2.928                0.000              167.774                5.073      1.677              0.576              0.000              0.000       -9.448                 -1.014       475.903   931SCORE:       0.000       4.848      2.000      0.304    -14.027      3.482      2.459                0.000              168.533                3.780      1.627              0.601              0.000              0.000       -0.605                 -0.044       659.559  1362

        SCORE:       0.000       9.305      0.000      0.033    -16.859      6.064      6.220                0.000              167.724                7.687      1.420              0.884              0.000              0.000        9.396                  0.598       859.740  1572SCORE:       0.000       7.578      1.000      0.315    -11.290      3.413      2.792                0.000              168.437                5.140      1.603              0.650              0.000              0.000       11.870                  0.718       751.594  1652

        Program is generating 100  structures but I am not sure how to interpret this data. Shall I use I_sc only?

         

        I also use Rosie server but it is giving an error message. Here is the link for job ID:  http://rosie.rosettacommons.org/snug_dock/viewjob/56601

        Thank you

        SS

        (screenshot is attached)

      • December 10, 2018 at 11:21 pm #14530
        Anonymous

          We are working on getting the full log for the ROSIE failure.  I can read that structure just fine in Rosetta. 

          Can you post your full cmd-line input to snugdock?

        • December 11, 2018 at 4:47 pm #14534
          Anonymous

            Locally it is running fine. I use two different trials

            1.

            mpiexec -np 8 $ROSETTA3/bin/snugdock.mpi.linuxgccrelease -in:file:s HLChain_B.pdb -ex1 -ex2 -partners LH_B -docking:dock_rtmin -nstruct 100 > log

             

            2. and also with flag

            ### JOB IO

            -s HLChain_B.pdb

            #-native HLChain_B.pdb # if available

            -out:prefix DOCKING_

            -out:file:scorefile score_out_snugdock.sc

            #-out:path:pdb models_path_out/

            -out:pdb_gz # gzip models for space

            -nstruct 100 # adequate sampling

            -ignore_zero_occupancy false

            -ignore_unrecognized_res

            -multiple_processes_writing_to_one_directory

            ### Docking

            -partners HL_B

            -spin

            -dock_pert 3 8

            ### do not filter for h3, constraint takes care of this geom

            -h3_filter false

            ### loop modeling settings

            #

            # KIC

            -kic_rama2b

            -loops:ramp_fa_rep

            -loops:ramp_rama

            -kic_omega_sampling

            -allow_omega_move true

            -loops:refine_outer_cycles 3

            -loops:max_inner_cycles 80

            # CCD (exit with ptr error)

            #-antibody:centroid_refine refine_ccd

            #-antibody:refine refine_ccd

            #-loops:outer_cycles 5

            #more standard settings, for packages used by antibody_H3

            -ex1

            -ex2aro

            -score:weights talaris2014

            -corrections::restore_talaris_behavior true

            # Disulphide

            -detect_disulf false

             

             

            But in both run snugdock score is 0.000 and rest of the print is fine.

            Thanks for your prompt reply.

            S

            • December 13, 2018 at 10:25 pm #14541
              Anonymous

                Ok, so – its definitely a bug.  The code was recently refactored and a stage in it AFTER docking is inadvertently clearing the pose energies cache.  Simple fix, but it requires some coding to do – as basically the pose needs to be re-scored.  Thanks for bringing this to our attention.  I’ll be able to get a pull request up tomorrow and it should be released next week.  Once I have the code working, I can walk you through changing it locally if you don’t want to wait for the next weekly release. 

                 

                Cheers,

                -Jared

              • January 3, 2019 at 5:08 pm #14554
                Anonymous

                  Happy New Year

                   

                  Any update?

                  -S

              • December 12, 2018 at 10:06 pm #14536
                Anonymous

                  Jared,

                  Any idea so far?

                  Thanks

                  S

                   

                  • December 12, 2018 at 11:43 pm #14537
                    Anonymous

                      Nothing out of the ordinary from your flags.  I’ll be able to dive into the code later this week. BTW, did you try the pre-pack locally?  It seems that is what was failing for snugdock on ROSIE.  Should have something on the scoring by Friday. 

                  • December 13, 2018 at 7:30 pm #14540
                    Anonymous

                       

                      Predock is working fine. I think ROSIE is failing because of occupancy cols are zero.  If you use this flag  -ignore_zero_occupancy then it will work.

                      $ROSETTA3/bin/docking_protocol.linuxgccrelease -in:file:s HLChain_B.pdb -ex1 -ex2 -partners LH_B -docking:dock_rtmin -ignore_zero_occupancy false

                       

                      Working PDB file is also attached.

                      Thanks a lot for your time.

                  • Author
                    Posts
                  Viewing 4 reply threads
                  • You must be logged in to reply to this topic.