loop model error

Member Site › Forums › Rosetta 3 › Rosetta 3 – General › loop model error

  • This topic has 21 replies, 4 voices, and was last updated 9 years ago by Anonymous.
Viewing 7 reply threads
  • Author
    Posts
    • April 3, 2011 at 7:26 am #848
      Anonymous

        Dear:
        I am trying to run the loop model protocol by the command: loopmodel.linuxgccrelease @kic.options

        However, it doesn’t work, and here is my log file. I would be very appreciated if you can give me some advices.

        By the way, does the loop protocol support MPI?

        Thank you very much

        log

        core.init: Mini-Rosetta version exported from unknown
        core.init: command: loopmodel.linuxgccrelease @kic.options
        core.init: ‘RNG device’ seed mode, using ‘/dev/urandom’, seed=-183596786 seed_offset=0 real_seed=-183596786
        core.init.random: RandomGenerator:init: Normal mode, seed=-183596786 RG_type=mt19937
        core.init: found database environment variable ROSETTA3_DB: /soft/rosetta-3.2.1/rosetta_database
        protocols::loopbuild: ==== Loop protocol: =================================================
        protocols::loopbuild: remodel perturb_kic
        protocols::loopbuild: intermedrelax no
        protocols::loopbuild: refine refine_kic
        protocols::loopbuild: relax fastrelax
        Warning: Unable to locate database file chemical/residue_type_sets/centroid

        ERROR: Unable to open file: ./chemical/residue_type_sets/centroid/residue_types.txt

        ERROR:: Exit from: src/core/chemical/ResidueTypeSet.cc line: 96

        log

      • April 3, 2011 at 5:01 pm #5275
        Anonymous

          “
          Warning: Unable to locate database file chemical/residue_type_sets/centroid

          ERROR: Unable to open file: ./chemical/residue_type_sets/centroid/residue_types.txt”

          You forgot to pass the -database flag.

          Loop modeling does not run under JD2 and thus doesn’t use MPI in the standard fashion. I am fairly, but not 100%, certain that it is MPI compatible anyway, it just doesn’t use the same flags, etc. I don’t think it has any MPI “options” at all – it’s either MPI or not.

        • April 5, 2011 at 9:00 pm #5279
          Anonymous

            Thanks for reply. It seems to work now if I add the option in command line. but it is said:

            ERROR: LoopRebuild::ERROR Loop definition out of boundary

            ERROR:: Exit from: src/protocols/loops/Loops.cc line: 594

            I define my loop in the loop.option as the following:
            LOOP 165 176 0 0 0

            I don’t know what’s wrong with it…..

            THX

          • April 6, 2011 at 3:10 pm #5286
            Anonymous

              The loop file format very unintuitively uses from-1 indexing, not PDB numbering. If you wanted the loop to run from PDB residues 165-176, you need to figure out what the residue indices for those residues are, starting from 1. If PDB residue 165 is the 50th residue in your PDB, then you’d use loop file:

              LOOP 50 61 0 0 0

              Does that make sense?

            • April 7, 2011 at 12:28 am #5295
              Anonymous

                A) it’s jran, not jrun – the typo may have been the problem?

                B) 12 may be out of range for jran – try numbers in the millions

                C) I’ve used constant_seed and jran with loop modeling before, I think it should work.

                D) If you use constant_seed alone, does it report the RNG seed as 1111111111 (plus or minus a few 1s)? That’s the “constant_seed” if you don’t also use jran.

              • April 7, 2011 at 2:36 pm #5301
                Anonymous

                  If you are “setting coordinates to 0 0 0”, then you probably need to be using the build_initial loop modeling option. Kinematic loop closure (as implemented) can’t take a nonexistent loop and solve for it, it only remodels existing loops. The build_initial option can create loops from 0,0,0 coordinates.

                • April 7, 2011 at 6:46 pm #5309
                  Anonymous

                    I’m assuming that is a silent file. You can try extract_pdbs, which is one of the Rosetta applications.

                    Generally speaking, the one with the lowest score is the best one, after applying your biophysical intuition and any experimental data you may have.

                  • November 19, 2015 at 7:08 pm #11333
                    Anonymous

                      Hello.

                      I think I’m having the same problem actually did not understand exactly how the loopfile configuration. follow the instructions of a tutorial, and still got this error message

                      protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active … 

                      basic.resource_manager.locator.FileSystemResourceLocator: Unable to open file ‘3vvt.loop’ at any of the following paths:

                      basic.resource_manager.locator.FileSystemResourceLocator:       3vvt1.loop

                      protocols.jd2.JobDistributor: 

                      [ERROR] Exception caught by JobDistributor for job 3rvyCH1ModeloHomoS_0001unable to open file 3rvyCH1.loop

                      protocols.jd2.JobDistributor: 

                      protocols.jd2.JobDistributor: 3rvyCH1ModeloHomoS_0001 reported failure and will NOT retry

                      basic.resource_manager.locator.FileSystemResourceLocator: Unable to open file ‘3vvt1.loop’ at any of the following paths:

                      basic.resource_manager.locator.FileSystemResourceLocator:       3vvt1.loop

                      protocols.jd2.JobDistributor: 

                       

                      tutorial instructions

                      Create a Rosetta Loops File:

                      The 1u19A.loops file are already provided in the

                      ~/rosetta_workshop/tutorials/protein_modeling/input_model

                      directory.

                      1. Create a file called 1u19A.loops in my_model

                      2. Use a visualization tool to help you determine loop start and end residue numbers. For example, you can use

                      “pymol 1u19A_on_2rh1A.pdb” and show-as ribbon to visualize what residues connect loop regions to helix.

                      3. Create one line per loop to be built:

                      LOOP 31 38

                      LOOP 67 74

                      LOOP 106 118

                      LOOP 139 169

                      LOOP 200 216

                      LOOP 244 252

                       

                      And here is my loopfile

                      LOOP 50 54

                      LOOP 107 117

                      LOOP 174 184

                      LOOP 217 220

                      LOOP 345 349

                      LOOP 402 413

                      LOOP 470 473

                      LOOP 506 511

                      LOOP 634 637

                      LOOP 690 704

                      LOOP 763 766

                      LOOP 799 804

                      LOOP 927 931

                      LOOP 984 1003

                      LOOP 1060 1070

                      LOOP 1103 1130

                      Some one could be help me?

                    • April 6, 2011 at 7:44 pm #5292
                      Anonymous

                        Thanks a lot for your kind reply.
                        In fact, the first residue in my PDB file is number one, so the number is consistent with actually it is… There are 300 aa in the PDB file, so 165-176 is make sense. I don’t know why it still says:

                        log

                        loops: ERROR invalid loop 165 176 0: End more than nres(0)
                        ERROR: LoopRebuild::ERROR Loop definition out of boundary
                        ERROR:: Exit from: src/protocols/loops/Loops.cc line: 594

                        BTW, I put the option -database /soft/rosetta-3.2.1/database in kic.options file, rosetta cannot recognize it. While it works when it specify in command line

                      • April 6, 2011 at 8:30 pm #5293
                        Anonymous

                          Problem solved.
                          I forget to set the loop coordinate to 0 0 0.

                          However, here is a new problem: since this loop protocol don’t support MPI. I try to use different seed in various CPU, but it seems that this protocol cannot recognize the option….. I try to add

                          -run:jrun 12
                          -run:constant_seed

                          in both command and option file, neither of them works. Is there other way to faster this task?

                          THX

                        • April 7, 2011 at 11:10 am #5298
                          Anonymous

                            Thank you very much. The seeds works now.But it still cannot generate models. it is said:

                            log

                            core.io.pdb.file_data: [ WARNING ] can’t find atom for res 1 atom OG (trying to set temp)
                            core.io.pdb.file_data: [ WARNING ] can’t find atom for res 4 atom CD1 (trying to set temp)
                            core.io.pdb.file_data: [ WARNING ] can’t find atom for res 4 atom CD2 (trying to set temp)
                            core.io.pdb.file_data: [ WARNING ] can’t find atom for res 4 atom CE1 (trying to set temp)
                            core.io.pdb.file_data: [ WARNING ] can’t find atom for res 4 atom CE2 (trying to set temp)
                            core.io.pdb.file_data: [ WARNING ] can’t find atom for res 4 atom CG (trying to set temp)
                            core.io.pdb.file_data: [ WARNING ] can’t find atom for res 4 atom CZ (trying to set temp)
                            core.io.pdb.file_data: [ WARNING ] can’t find atom for res 4 atom OH (trying to set temp)
                            core.io.pdb.file_data: [ WARNING ] can’t find atom for res 5 atom CD1 (trying to set temp)
                            core.io.pdb.file_data: [ WARNING ] can’t find atom for res 5 atom CD2 (trying to set temp)
                            core.io.pdb.file_data: [ WARNING ] can’t find atom for res 5 atom CG (trying to set temp)
                            core.io.pdb.file_data: [ WARNING ] can’t find atom for res 6 atom CD1 (trying to set temp)
                            core.io.pdb.file_data: [ WARNING ] can’t find atom for res 6 atom CD2 (trying to set temp)
                            core.io.pdb.file_data: [ WARNING ] can’t find atom for res 6 atom CE1 (trying to set temp)
                            core.io.pdb.file_data: [ WARNING ] can’t find atom for res 6 atom CE2 (trying to set temp)
                            core.io.pdb.file_data: [ WARNING ] can’t find atom for res 6 atom CG (trying to set temp)
                            core.io.pdb.file_data: [ WARNING ] can’t find atom for res 6 atom CZ (trying to set temp)
                            core.io.pdb.file_data: [ WARNING ] can’t find atom for res 7 atom CD1 (trying to set temp)
                            core.io.pdb.file_data: [ WARNING ] can’t find atom for res 7 atom CD2 (trying to set temp)
                            core.io.pdb.file_data: [ WARNING ] can’t find atom for res 7 atom CG (trying to set temp)
                            core.io.pdb.file_data: [ WARNING ] can’t find atom for res 8 atom CG (trying to set temp)
                            core.io.pdb.file_data: [ WARNING ] can’t find atom for res 8 atom OD1 (trying to set temp)
                            core.io.pdb.file_data: [ WARNING ] can’t find atom for res 8 atom OD2 (trying to set temp)
                            core.io.pdb.file_data: [ WARNING ] can’t find atom for res 9 atom CD (trying to set temp)
                            core.io.pdb.file_data: [ WARNING ] can’t find atom for res 9 atom CG1 (trying to set temp)
                            core.io.pdb.file_data: [ WARNING ] can’t find atom for res 9 atom CG2 (trying to set temp)
                            core.io.pdb.file_data: [ WARNING ] can’t find atom for res 10 atom CD (trying to set temp)
                            core.io.pdb.file_data: [ WARNING ] can’t find atom for res 10 atom CG1 (trying to set temp)
                            core.io.pdb.file_data: [ WARNING ] can’t find atom for res 10 atom CG2 (trying to set temp)
                            core.io.pdb.file_data: [ WARNING ] can’t find atom for res 11 atom CG2 (trying to set temp)
                            core.io.pdb.file_data: [ WARNING ] can’t find atom for res 11 atom OG1 (trying to set temp)
                            core.io.pdb.file_data: [ WARNING ] can’t find atom for res 12 atom CD1 (trying to set temp)
                            core.io.pdb.file_data: [ WARNING ] can’t find atom for res 12 atom CD2 (trying to set temp)
                            core.io.pdb.file_data: [ WARNING ] can’t find atom for res 12 atom CE1 (trying to set temp)
                            core.io.pdb.file_data: [ WARNING ] can’t find atom for res 12 atom CE2 (trying to set temp)
                            core.io.pdb.file_data: [ WARNING ] can’t find atom for res 12 atom CG (trying to set temp)
                            core.io.pdb.file_data: [ WARNING ] can’t find atom for res 12 atom CZ (trying to set temp)
                            core.io.pdb.file_data: [ WARNING ] can’t find atom for res 12 atom OH (trying to set temp)
                            core.io.pdb.file_data: [ WARNING ] can’t find atom for res 13 atom CD1 (trying to set temp)
                            core.io.pdb.file_data: [ WARNING ] can’t find atom for res 13 atom CD2 (trying to set temp)
                            core.io.pdb.file_data: [ WARNING ] can’t find atom for res 13 atom CG (trying to set temp)
                            core.io.pdb.file_data: [ WARNING ] can’t find atom for res 14 atom CG1 (trying to set temp)
                            core.io.pdb.file_data: [ WARNING ] can’t find atom for res 14 atom CG2 (trying to set temp)
                            core.io.pdb.file_data: [ WARNING ] can’t find atom for res 15 atom CD1 (trying to set temp)
                            core.io.pdb.file_data: [ WARNING ] can’t find atom for res 15 atom CD2 (trying to set temp)
                            core.io.pdb.file_data: [ WARNING ] can’t find atom for res 15 atom CE1 (trying to set temp)
                            core.io.pdb.file_data: [ WARNING ] can’t find atom for res 15 atom CE2 (trying to set temp)
                            core.io.pdb.file_data: [ WARNING ] can’t find atom for res 15 atom CG (trying to set temp)
                            core.io.pdb.file_data: [ WARNING ] can’t find atom for res 15 atom CZ (trying to set temp)
                            core.io.pdb.file_data: [ WARNING ] can’t find atom for res 17 atom CG1 (trying to set temp)
                            core.io.pdb.file_data: [ WARNING ] can’t find atom for res 17 atom CG2 (trying to set temp)
                            core.io.pdb.file_data: [ WARNING ] can’t find atom for res 18 atom CG2 (trying to set temp)
                            core.io.pdb.file_data: [ WARNING ] can’t find atom for res 18 atom OG1 (trying to set temp)
                            core.io.pdb.file_data: [ WARNING ] can’t find atom for res 19 atom CD1 (trying to set temp)
                            core.io.pdb.file_data: [ WARNING ] can’t find atom for res 19 atom CD2 (trying to set temp)
                            core.io.pdb.file_data: [ WARNING ] can’t find atom for res 19 atom CE1 (trying to set temp)
                            core.io.pdb.file_data: [ WARNING ] can’t find atom for res 19 atom CE2 (trying to set temp)
                            core.io.pdb.file_data: [ WARNING ] can’t find atom for res 19 atom CG (trying to set temp)
                            core.io.pdb.file_data: [ WARNING ] can’t find atom for res 19 atom CZ (trying to set temp)
                            core.io.pdb.file_data: [ WARNING ]
                            .
                            .
                            .
                            .
                            .
                            .
                            protocol.loops.LoopMover: Setting extended torsions: LOOP 64 75 73 0 1
                            protocol.loops.LoopMover: Building Loop: LOOP 64 75 73 0 1
                            protocol.loops.LoopMover: Building Loop attempt: 0
                            protocol.loops.LoopMover: perturb_one_loop_with_KIC: 64 12
                            protocol.loops.LoopMover: remodel init temp: 2
                            protocol.loops.LoopMover: remodel final temp: 1
                            protocol.loops.LoopMover: kinematic initial perturb with start_res: 64 middle res: 69 end_res: 75
                            protocol.loops.LoopMover: loop rmsd before initial kinematic perturbation:0
                            protocol.loops.LoopMover: Attempting loop building: 0 …
                            protocol.loops.LoopMover: Attempting loop building: 1 …
                            protocol.loops.LoopMover: Attempting loop building: 2 …
                            protocol.loops.LoopMover: Attempting loop building: 3 …
                            protocol.loops.LoopMover: Attempting loop building: 4 …
                            protocol.loops.LoopMover: Attempting loop building: 5 …
                            protocol.loops.LoopMover: Attempting loop building: 6 …
                            protocol.loops.LoopMover: Attempting loop building: 7 …
                            protocol.loops.LoopMover: Attempting loop building: 8 …
                            protocol.loops.LoopMover: Attempting loop building: 9 …
                            protocol.loops.LoopMover: Attempting loop building: 10 …
                            .
                            .
                            .
                            .
                            .
                            can’t find atom for res 20 atom CG1 (trying to set temp)

                            protocol.loops.LoopMover: [WARNING] Failed to build loop with kinematic Mover during initial kinematic perturbation after 100 trials: LOOP 64 75 64 0 1
                            protocol.loops.LoopMover: Unable to build this loop – a critical error occured. Moving on ..
                            protocol.loops.LoopMover: Loopstat: 64 75 64 75 12 time 6.5 1 time 6.5 1e+07 ext
                            protocols.looprelax: Structure failed initial kinematic closure. Skipping…
                            protocols::checkpoint: Deleting checkpoints of Remodel
                            protocols::checkpoint: Deleting checkpoints of Loopbuild

                          • April 7, 2011 at 6:31 pm #5308
                            Anonymous

                              Thank you very much. It works fine now.
                              I’ve just got a question, the output file is a loops.out, How can I convert it to PDB file? and how can I know which one is the best one?

                              THX

                            • April 7, 2011 at 7:10 pm #5310
                              Anonymous

                                I use the command
                                extract_pdbs.linuxgccrelease -in:file:silent loops.out -database /soft/rosetta-3.2/database

                                but I don’t see the score files……

                              • April 7, 2011 at 7:54 pm #5311
                                Anonymous

                                  It is really strange, I add the following options in my kic.options file and none of them works:
                                  -out:file:scorefile score.sc
                                  -out:suffix aa

                                  there is no score.sc file generated. the output suffix is not aa_001.pdb but just _001.pdb

                                • April 7, 2011 at 8:01 pm #5312
                                  Anonymous

                                    Are you trying to generate pdb files or score files or silent files?

                                    Exactly what outputs did you get from loop modeling? What file types were they (you can just cut-and-paste a sample)?

                                  • April 7, 2011 at 8:13 pm #5313
                                    Anonymous

                                      I use out:file:pdb for output, and it generate PDB files.

                                      here is some of the log:
                                      protocols.relax.FastRelax: CMD: accept_to_best -538.711 1.85429 1.85429 0.44
                                      protocols.relax.FastRelax: CMD: endrepeat -538.711 1.85429 1.85429 0.44
                                      protocols::checkpoint: Deleting checkpoints of FastRelax
                                      protocols::checkpoint: Deleting checkpoints of FastRelax
                                      protocols.looprelax: ====================================================================================
                                      protocols.looprelax: ===
                                      protocols.looprelax: === Getting Statistics
                                      protocols.looprelax: ===
                                      protocols.looprelax: ===
                                      protocols::checkpoint: Deleting checkpoints of Loopbuild
                                      protocols::loopbuild: loop_cenrms: 0
                                      protocols::loopbuild: loop_rms: 0
                                      protocols::loopbuild: total_energy: -544.583
                                      protocols::loopbuild: chainbreak: 0.0171348

                                    • April 7, 2011 at 8:21 pm #5314
                                      Anonymous

                                        OK, I misunderstood you before. You HAVE PDB files, and WANT scores. Run the score application (score_jd2, perhaps?). The total_score is right there in your log file, but it’s challenging to extract from there. The same total_score number may be at the end of each PDB file (where you can grep it out). Running score will get you more useful per-residue and per-term scores.

                                        It’s almost criminal that the loop modeling code (which has already calculated all these scores) doesn’t automatically output them for you…

                                      • April 7, 2011 at 8:27 pm #5315
                                        Anonymous

                                          yes, you are right. here is my full option, do you have any suggestion for solving this by add option to it? I think it would be more reliable if it generate the score file during the model steps.

                                          -nstruct 10 #number of models to build. 1000 recommended for production runs.
                                          -loops:input_pdb input.pdb
                                          -loops:loop_file input.loops
                                          -loops:relax fastrelax
                                          -loops:extended #force phi-psi angles to be set to 180 degrees independent of loop input file (recommended for production runs)
                                          -loops:remodel perturb_kic
                                          -loops:refine refine_kic
                                          -ex1 #Include extra chi1 rotamers
                                          -ex2
                                          #-out:file:silent_struct_type binary #output file type
                                          out:file:pdb
                                          -out:suffix aa
                                          -out:file:scorefile score.sc

                                          -out:file:fullatom #output file will be fullatom

                                        • April 7, 2011 at 8:54 pm #5316
                                          Anonymous

                                            If out:file:scorefile didn’t work, it’s probably not going to. The total score should be at the end of the PDB file (you can do “grep -H total_energy *pdb” to get the scores out) or use the score app.

                                          • November 24, 2015 at 10:04 pm #11340
                                            Anonymous

                                              What’s you loop file named? Is it ‘3vvt1.loop’ ? What directory is it in? Is it in the local directory (that is, the directory the Rosetta command is being run from.

                                              If the file is correctly named and in the correct location, it might be that there is a non-printing character in your options file. Common issues include line ending issues between Windows and Unix, where Windows will insert an extra character which can mess up Unix file reading – so you may be trying  to open ‘3vvt1.loop^M’ instead of ‘3vvt1.loop’, where the ‘^M’ is an invisible (non-printing) character.

                                              You can check to see if there’s an issue with the file by using the ‘-v’ option of cat to make the non-printing characters visible:

                                              cat -v options.file

                                              If it’s a particularly long file, you can diff with and without the -v to see which lines are different

                                              diff <(cat options.file)  <(cat -v options.file)

                                              If it is a ‘^M’ line ending issue, then you can use the dos2unix program to fix it.

                                            • December 18, 2015 at 2:57 am #11380
                                              Anonymous

                                                Thanks RMORETTI

                                                That is the new msg error!!!

                                                ERROR: Residue index description given on line 0 of the file named 3rvyCH1.loop exceeds the number of residues in the Pose: pose_index_ = 927 vs pose.total_residue() 884

                                                ERROR:: Exit from: src/protocols/loops/LoopsFileIO.cc line: 157

                                                My script

                                                -in:file:s 3rvyA.pdb

                                                -in:file:fullatom

                                                -in:file:spanfile 3rvyCH1.span

                                                -out:file:silent_struct_type binary

                                                -out:file:silent 3rvyCH1.out

                                                -out:prefix 3rvyCH1test

                                                -out:file:fullatom

                                                -nstruct 3

                                                -loops:relax fastrelax

                                                -loops:extended true

                                                -loops:idealize_after_loop_close

                                                -loops:fast

                                                -ex1

                                                -ex2

                                                -loops:frag_sizes 9 3 1

                                                -loops:frag_files 3rvyCH1_09_05.200_v1_3 3rvyCH1_03_05.200_v1_3 none

                                                -loops:remodel quick_ccd

                                                -loops:ccd_closure

                                                -loops:refine refine_kic

                                                -loops:random_loop

                                                -membrane:no_interpolate_Mpair

                                                -membrane:Menv_penalties

                                                -score:weights membrane_highres_Menv_smooth.wts

                                                -out:path:pdb /pdb2/

                                                what could be that?

                                              • December 18, 2015 at 10:26 pm #11383
                                                Anonymous

                                                  The loops file is Pose-numbered, rather than PDB numbered. That is, the numbering in the loops file is such that it assumes that the first residue in your structure is residue 1, and it goes up by one for each residue, regardless of gaps or different chains. It *isn’t* the same as the residue number in the PDB file.

                                                  As a general rule of thumb, if a residue number in Rosetta is just a plain number, without a chain letter, it’s in Pose numbering. If the residue specification comes with  a chain letter, then it’s in PDB numbering. 

                                              • Author
                                                Posts
                                              Viewing 7 reply threads
                                              • You must be logged in to reply to this topic.