Reply To: disulfide bonds using abinitio folding module

[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