Local Haddock run - The following floating-point exceptions are signalling: IEEE_DIVIDE_BY_ZERO

HADDOCK
1

Hello,
I am currently attempting to perform an ab-initio DNA-Protein docking. I was testing with a PDB file from PDB, that I split into individual nucleotide and protein files.
The process ran up until:
‘’’
Note: The following floating-point exceptions are signalling: IEEE_DIVIDE_BY_ZERO

calculating structure 12
  queue command:
 ------------------------------------------------------------

Structure 2: running
Structure 3: running
Structure 4: running
Structure 5: running
Structure 6: running
Structure 7: running
Structure 8: running
Structure 9: crashed
Structure 10: running
Structure 11: running
Structure 12: running
‘’’

The FAILED file displayed the following repeatedly:
‘’’
%EVALUATE-ERR: EVALUATE assignment aborted.:
evaluate ($resid2=encode(decode($resid1)+1))
^
%XRDECODE-ERR: Illegal argument(s).:
evaluate ($resid2=encode(decode($resid1)+1))

%PARSER error encountered: Encountered too many parsing errors.
‘’’
I don’t understand what this could mean, and haven’t yet found references on it.
I would greatly appreciate some help!
Thank you in advance !!

2

CNS is stopping because of too many parsing errors. This points to possible errors in run.cns (e.g. missing quotes and such)

Check carefully the file you must have edited

3

Hello, thank you so much for your quick response !
I checked all the fields I initially modified for ‘syntax’ errors, and haven’t found any.
I attempted a fresh run, modifying carefully the required parameters and it led to the same result.
After some attempts,I tried with another complex and it worked.
I suspect it was due to PDB formatting, would that make sense?

4

Yes - bad PDB format will also cause issues…

Best to check and fix the PDB format with our pdb-tools

5

Indeed it was an insert error;
pdb_fixinsert, solved it !!

Thank you so much!