“caught exception” for PDB with membrane “DUM” residues

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    • May 30, 2018 at 3:35 pm #2928
      Anonymous

        If I run this command:

        residue_energy_breakdown.static.linuxgccrelease -in:file:s hasDUMresidues.pdb -out:file:silent energy_breakdown.out -ignore_unrecognized_res true

        on the attached pdb, I get this error:

        caught exception 

         

        File: src/core/id/NamedAtomID_Map.hh:390

        Residue outside res_map range

         

        It seems like Rosetta recognizes “DUM”, but maybe my DUM doesn’t match Rosetta’s pdb_DUM? If I delete all the DUM residues, then the error goes away. I also tried deleting all but one of the DUM residues, but it still failed, making it seem like the problem isn’t too many DUM residues.

         

        Can someone give me some clarity on what exactly the problem is here?

        Thanks!

        Here’s the version of Rosetta I’m using (it’s labeled “3.9” on my cluster):

        core.init: Rosetta version: rosetta.binary.linux.release-171 r171 2018.09+release.333d996 333d99699777cd6a50d1c1736bacd689f8f1d1df https://www.rosettacommons.org 2018-02-27T09:57:00.705373

      • May 30, 2018 at 6:15 pm #14250
        Anonymous

          > maybe my DUM doesn’t match Rosetta’s pdb_DUM?

          That’s certainly the first thing to look at.  Your access to pdb_DUM is coming from the PDB Chemical Components dictionary (CCD).  Unfortunately you are going to have a bad time with its DUM residue: https://www3.rcsb.org/ligand/DUM  it’s a DUMmy residue.  

          Whatever your DUM is, you probably need to make parameters for it (molfile_to_params, look around the forums / dox for how to use it) or rename your residue to whatever it is in the PDB CCD as applicable.  You may or may not also need to disable PDB CCD loading, it’s something like “-load_chemical_components false”, if that’s not quite right and you can’t find the option i’ll look harder.

        • April 28, 2020 at 5:51 pm #15255
          Anonymous

            I recieved the same error in a different circumstance but was able to fix it.

            My issue was the Ligand file, LIG.pdb I was using has the wrong atom names.

            ie) H  or C instead of H1 or C1. See Here: https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/pdbintro.html

            Correcting this fixes the error, perhaps try this with your hasDUMresidues.pdb.

            A quick way to fix it  without doing it all manually or with ‘sed’ commands would be to run it through the Charmm input generator at http://www.charmm-gui.org/?doc=input/pdbreader , parameterizing with whatever FF (you wont be using this part of it) and downloading the step1_pdbreader.pdb file and then doing: 

            mv step1_pdbreader.pdb hasDUMresidues.pdb

            Now this worked for me, but your situation maay be different; just my 2 cents!

            – Andrew

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