rosetta.script segmentation fault

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    • #1660

        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


      • #9368

          felipet, can you post your script?

        • #9369


            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:jump_move true
            -default_max_cycles 200
            -relax:min_type lbfgs_armijo_nonmonotone
            -relax:jump_move true
            -score:weights stage3_rlx.wts
            -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

          • #9377

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



            • #9413

                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.

                Frank Dimaio may be be able to help, as he wrote most of the Cartesian code.

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