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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    • #1890

        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 -mute -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/ 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.


      • #10519

          Were you able to solve this?
          You probably created your params file with a newer version of Rosetta, which made a following change:
          old version: BOND atom1 atom2
          new version (post 081514): BOND_TYPE atom1 atom2 bondtype
          Since you are still using Rosetta3.5, you get the error which you see.
          You can either make your params file with rosetta3.5, or use an executable from the same version of Rosetta that was used to create params file.

          Hope that works.

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