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"caught exception" for PDB with membrane "DUM" residues

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"caught exception" for PDB with membrane "DUM" residues
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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

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Wed, 2018-05-30 08:35
nitroamos

> 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.

Wed, 2018-05-30 11:15
smlewis