Ligand docking: ERROR: set_atom_base: atoms must be bonded!

Member Site Forums Rosetta 3 Rosetta 3 – Applications Ligand docking: ERROR: set_atom_base: atoms must be bonded!

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    • #1891
      Anonymous

        Hi,
        I’m new in rosetta docking. I ran this command
        /farm/software/rosetta3.5/rosetta_source/bin/rosetta_scripts.linuxgccrelease -database /farm/software/rosetta3.5/rosetta_database/ -run:constant_seed -run:rng mt19937 -overwrite -no_optH -ex1 -ex1aro -ex2 -mute core.util.prof -mute core.io.database -run:preserve_header -in:file:s RCL+LMP.pdb -extra_res_fa LMP.fa.params -extra_res_cen LMP.cen.params -parser:protocol ligand_dock_LMP.xml -enzdes:cstfile LMP.cst -nstruct 3 > output.log
        and it was stopped by
        ERROR: set_atom_base: atoms must be bonded!
        ERROR:: Exit from: src/core/chemical/ResidueType.cc line: 767

        Could anyone help me with this problem? This has something to do with the structure or the rosetta setting?
        Many thanks. :)

        P.s. Attached is the output.log file.

        Meng

      • #10052
        Anonymous

          How did you generate your params file, and what does it look like? The most likely cause of this issue is a bad params file.

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