Problems in Loop Modeling

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    • #349


        I am trying to build a loop model with the last release of rosseta, and I get the following error:

        protocols.looprelax: ==== Loop protocol: =================================================
        protocols.looprelax: remodel perturb_ccd
        protocols.looprelax: intermedrelax no
        protocols.looprelax: refine refine_ccd
        protocols.looprelax: relax no
        loops: ERROR invalid loop 271 288 279: End more than nres(0)

        ERROR: LoopRebuild::ERROR Loop definition out of boundary

        ERROR:: Exit from: src/protocols/loops/ line: 699

        my loops file is:

        LOOP 270 288 279

        my flag’s file:

        -loops::input_pdb t000/t000.template.pdb
        -loops::loop_file t000/t000.pose_loops
        -loops::frag_sizes 9 3
        -loops::frag_files t000/aat000_09_05.200_v1_3 t000/aat000_03_05.200_v1_3
        -loops::build_initial false
        -loops::remodel perturb_ccd
        -loops::refine refine_ccd

        I belive that my problem is in this nres(0), checking the code i found that the this nres== 0 value is coming from:

        Size nres = pose.total_residue();

        Can anybody give some help??

        Thanks very much in advance!

      • #4239

          Does t000.template.pdb contain residues? I’m not trying to be flippant – the obvious answer if you have 0 residues is that you simply don’t have any residues in the protein. You can (and should) try passing a different protein to see if it behaves differently, or manually tweaking the template PDB. You can try deleting atoms from some of the sidechains (or mainchain); this will cause the PDB reader to spit warnings, so you can verify that it’s reading the PDB it’s supposed to read.

        • #4244

            Thanks very much smlewis,

            after a while trying and trying i found the problem, and i write it here in case it can help someone who is stacked as i was:

            DO NOT PUT CHARGES AND RADII TO YOUR PDB FILE, older versions of rosetta had no trubble dealing with files with charges and radii but this last version of rosetta will give my error if you put charges and radii to your pdb.

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