Misleading error message

[Anonymous]

Hi, when trying to relax a protein, I got the error message:

ERROR: unknown atom_name: ‘CZH’  in residue TRP

 

However, there was no atom with the name ‘CZH’ in that pdb, not in TRP or any other residue.

The problem turned out to be the following block:

ATOM      1  CAY GLU R  30      97.797  95.815  94.750  1.00  0.00      R

ATOM      2  HY1 GLU R  30      98.446  96.657  94.577  1.00  0.00      R

ATOM      3  HY2 GLU R  30      97.711  95.555  95.758  1.00  0.00      R

ATOM      4  HY3 GLU R  30      96.724  96.048  94.634  1.00  0.00      R

ATOM      5  CY  GLU R  30      98.193  94.826  93.766  1.00  0.00      R

ATOM      6  OY  GLU R  30      99.153  94.898  93.025  1.00  0.00      R

 

May I suggest to print the line from the pdb that is causing the error together with the error message?

That would be very helpful!

Thanks

PS: I use release 171 (2018.09)

[Anonymous]

That’s what the error message is saying: TRP has no atom named CZH, but some other user input has  Rosetta looking for atom CZH in a TRP residue.   Because the error isn’t a problem with the PDB file, there’s no relevant line to print.  Check your inputs, and remove whatever it is that’s telling Rosetta to look for a CZH atom in a TRP residue.  (If you need help finding this, please include the full output and your full inputs, so that we know what module is producing the error message.)

[Author]

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