disulfide bonds using abinitio folding module

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    • #447
      Anonymous

        Hi everybody,

        I’m trying to fold a protein sequence using the abinitio module in rosetta3. I know that two cysteins make a disulfide bond so I have tried to put distance constrains between CA atoms in a .cst file but the structures generated do not have this bond formed. How can I tell rosetta that two cys are forming a disulfide bond?

        Thanks a lot

      • #4362
        Anonymous

          There is a “disulfide file”, passed in via in::fix_disulf.

          Check the commentary for file core/io/raw_data/DisulfideFile.hh to see how it works. I’ve never used it.

          You may also need an option “abinitio::detect_disulfide_before_relax”.

        • #4363
          Anonymous

            > Hi everybody,
            >
            > I’m trying to fold a protein sequence using the abinitio module in rosetta3. I know that two cysteins make a disulfide bond so I have tried to put distance constrains between CA atoms in a .cst file but the structures generated do not have this bond formed. How can I tell rosetta that two cys are forming a disulfide bond?
            >
            > Thanks a lot

            I have a native structure and in the native structure I have the disulfide bond. I fix residues to native, I use a disulfide file giving -fix_disulf filename and -detect_disulfides in the flag file. I also use the cst file where I put some distance constrains but even like this during the folding the native conformation is not maintain and the disulfide bond is not there. I have also added cst_weigth 1000. I have taken a look to the log file and at the begining of the folding says: detected disulfide bond between residues 19 and 45 which is correct!!!
            Have any idea?

            thanks!!!

          • #4364
            Anonymous

              > Hi everybody,
              >
              > I’m trying to fold a protein sequence using the abinitio module in rosetta3. I know that two cysteins make a disulfide bond so I have tried to put distance constrains between CA atoms in a .cst file but the structures generated do not have this bond formed. How can I tell rosetta that two cys are forming a disulfide bond?
              >
              > Thanks a lot

              It seems that the program is not reading the cst_weights as in the score I can’t find the term of the constrains.
              My flag file is like this:
              -in:file:frag3 ../frag/aaTAGS_03_05.200_v1_3
              -in:file:frag9 ../frag/aaTAGS_09_05.200_v1_3
              -out:nstruct 6
              -detect_disulfides
              -disulf_filter true
              -fix_disulf ./disulf.ini
              -cst_weight 100000
              -norepack_disulf
              -abinitio:fix_residues_to_native 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97
              -database /home/fenollar/rosetta3/rosetta3_database/
              -constraints:cst_file ./TAGS_.cst
              -out:pdb

              the log finds the constrains files and the disulfide bond:

              core.conformation.Conformation: Found disulfide between residues 16 49
              core.pack.task: Packer task: initialize from command line()
              core.io.fragments: reading fragments from file: ../frag/aaTAGS_09_05.200_v1_3 …
              core.io.fragments: rosetta++ fileformat detected! Calling legacy reader…
              core.fragments.ConstantLengthFragSet: finished reading top 25 9mer fragments from file ../frag/aaTAGS_09_05.200_v1_3
              core.io.fragments: reading fragments from file: ../frag/aaTAGS_03_05.200_v1_3 …
              core.io.fragments: rosetta++ fileformat detected! Calling legacy reader…
              core.fragments.ConstantLengthFragSet: finished reading top 200 3mer fragments from file ../frag/aaTAGS_03_05.200_v1_3
              core.scoring.constraints: Constraint choice: ./TAGS_.cst
              core.io.constraints: read constraints from ./TAGS_.cst
              protocols.jumping: compute strand/loop fractions for 95 residues…
              protocols.abinitio.AbrelaxApplication: run ClassicAbinitio…..
              core.scoring.ScoreFunctionFactory: SCOREFUNCTION: standardcore.scoring.ScoreFunctionFactory: SCOREFUNCTION PATCH: score12

              and then the scoring file:

              SCORE: score vdw cenpack pair env cbeta rg hs_pair ss_pair rsigma sheet rms gdtmm maxsub clashes_total clashes_bb time us description
              SCORE: 61.237 14.810 -5.252 -11.644 -19.121 39.519 42.926 0.000 0.000 0.000 0.000 10.622 0.460 58.000 3.000 1.000 54.000 01 S_01_00000001

              so no constrains term.

              i would appreciate any help.

              THANKS!!!

              Cris

            • #4390
              Anonymous

                I asked around on the developer’s list and nobody knows quite what’s wrong. The best suggestion was to ignore the disulfide code and use an explicit AtomPairConstraint instead – perhaps the constraint weights will work properly if you remove the disulfide flags from the command line?

              • #4399
                Anonymous

                  Hi,

                  I had the same problem and using “-in:fix_disulf disulfidefile” in fullatom-mode without constraints and any other option regarding disulfides like “detect_disulfide_before_relax” it worked.

                  Just put the 2 numbers like 7 and 35 of the cysteines separated by a space-character and followed by a new-line (this seems to be necessary) in a text file and it should work!

                  Hope this helped!

                  JS

                  • #10785
                    Anonymous

                      Hi JS and Everyone,
                      It seems that JS’s method is simple to use. However, when I use

                      -fix_disulf /home/lanselibai/Cheng/20150121_minirosetta/input/disulfidefile

                      I have always been told “Segmentation fault (core dumped)” without any information in the log file.

                      The disulfidefile is as below:

                      23 88
                      (a new blank line)

                      I also DO NOT have constraints and other disulfide associated flags (e.g. -detect_disulfide_before_relax, -detect_disulfides, -disulf_filter, -norepack_disulf).

                      Can someone help me? Thank you very much.

                      Yours sincerely
                      Cheng

                  • #10788
                    Anonymous

                      So any time you get a Segmentation fault in a Rosetta release version, it’s a definite bug in Rosetta – at the very least it should give you an error message instead.

                      Could you put together a minimal example that shows that behavior, upload it to some file hosting server (DropBox or Google Drive or the like), and post a link here? I can take a look at it and see what might be going wrong.

                    • #10791
                      Anonymous

                        Hi R Moretti,
                        Nice to see you again. The link below contains all my files.

                        https://copy.com/GOaBvrz3tBb4JSz2

                        When the “-in:fix_disulf” is disabled, it works all fine.

                        Thank you very much.

                        Yours sincerely
                        Cheng

                      • #10820
                        Anonymous

                          The example you posted seems to work fine for me with a recent version of Rosetta, with or without the fix_disulf flag.

                        • #10835
                          Anonymous

                            Hi R Moretti,
                            Thank you. What is the version you are using? I just installed rosetta_src_2015.05.57576_bundle and tested it again. However, I was told “Segmentation fault (core dumped)” again and the attachment is the log file. All of the input files can be found at

                            https://copy.com/DZLN3Yti1BZnbVP4

                            Do you know why is that?

                            (In the beginning, I was told “-silent_decoytime not found in command line top-level context”. So I disable it)

                            Thank you very much.

                            Yours sincerely
                            Cheng

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