rosetta.script segmentation fault

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    • October 2, 2013 at 5:41 pm #1660
      Anonymous

        Dear all,

        I am trying to perform a comparative homology modelling with the following command line

        rosetta_scripts.linuxgccdebug @flags -database ~/rosetta_2013wk36_bundle/main/database/ -nstruct 10

        the rosetta scripts is:

        the error at the end of the output is:

        core.scoring.CartesianBondedEnergy: Creating new peptide-bonded energy container (82)
        rosetta_scripts.linuxgccdebug: src/utility/vectorL.hh:363: typename std::vector::reference utility::vectorL<, T, A>::operator[](typename utility::vectorL_IndexSelector<(L >= 0)>::index_type) [with int L = 1, T = utility::pointer::owning_ptr, A = std::allocator >]: Assertion `static_cast< size_type >( i – l_ ) < super::size()' failed.
        Got some signal… It is:6
        Process was aborted!

        I can’t understand why I get this error

        thanks in advance for any help

        felipet

      • October 2, 2013 at 6:45 pm #9368
        Anonymous

          felipet, can you post your script?

        • October 2, 2013 at 7:08 pm #9369
          Anonymous

            sorry,

            the script is attached

            and the flags I am using are:
            # i/o
            -in:file:fasta Inputs/t000_.fasta
            -in:file:psipred_ss2 Inputs/t000_.psipred_ss2
            -in:file:frag9 Inputs/aat000_09_05.200_v1_3
            -in:file:frag3 Inputs/aat000_03_05.200_v1_3
            -nstruct 10
            -parser:protocol rosetta_cm.xml
            -out:file:silent_struct_type binary

            # relax options
            -relax:minimize_bond_angles
            -relax:minimize_bond_lengths
            -relax:jump_move true
            -default_max_cycles 200
            -relax:min_type lbfgs_armijo_nonmonotone
            -relax:jump_move true
            -score:weights stage3_rlx.wts
            -use_bicubic_interpolation
            -hybridize:stage1_probability 1.0
            -sog_upper_bound 15
            #-mute all

            # reduce memory footprint
            -chemical:exclude_patches LowerDNA UpperDNA Cterm_amidation SpecialRotamer VirtualBB ShoveBB VirtualDNAPhosphate VirtualNTerm CTermConnect sc_orbitals pro_hydroxylated_case1 pro_hydroxylated
            _case2 ser_phosphorylated thr_phosphorylated tyr_phosphorylated tyr_sulfated lys_dimethylated lys_monomethylated lys_trimethylated lys_acetylated glu_carboxylated cys_acetylated tyr_diiodin
            ated N_acetylated C_methylamidated MethylatedProteinCterm

          • October 4, 2013 at 7:39 pm #9377
            Anonymous

              I also tried the pdb and alignment of the CM threading example in the test folder and it works,

              thanks

              felipet

            • October 14, 2013 at 3:31 pm #9413
              Anonymous

                Filipet, are you a developer?
                I’ve never used homology modelling in Rosetta; however the issue you are seeing looks to be coming from the CartesianMinimizer. Are you using 3.5/weekly or the developers trunk?

                If you remove these options, your bug should go away.
                -relax:minimize_bond_angles
                -relax:minimize_bond_lengths

                Frank Dimaio may be be able to help, as he wrote most of the Cartesian code.
                http://pages.cs.wisc.edu/~dimaio/

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