Tinker error for ethylbenzene

[flatstik]

Trying to run the program with ethylbenzene (smiles: CCc1ccccc1) and Carbon experimental data:

PyDP4.py -f mmff -w gnomesw -s chloroform -m t --Smiles ./ebb.smiles ./exper/test/

Running Tinker...
/appl/soft/chem/tinker/bin/scan Smiles_Mol_0_0 /appl/soft/chem/tinker/params/mmff.prm 0 10 20 0.00001 | tee ./Smiles_Mol_0_0.tout
Tinker job 1 of 1 completed.
Smiles_Mol_0_0 is matching conformational search output for Smiles_Mol_0_0
Reading Smiles_Mol_0_0
Tinker output Smiles_Mol_0_0 is corrupted, aborting.

Edit: same results with InChI. If I add other heteroatom there, it runs the program. Edit2:

CCCCc1ccccc1 <-- works CCCc1ccccc1 <-- doesn't work CCc1ccccc1 <-- doesn't work Cc1ccccc1 <-- doesn't work c1ccccc1 <--- doesnt't work

Basically anything smaller than CCCc1ccccc1 doesn't work.

[HowarthA]

I have added a small fix for this, let me know if this causes any other issues.

[flatstik]

It did cause other issues:

WARNING: NMR shift calculation currently ignores the instruction to exclude atoms from analysis
C shifts for isomer 0: 
20.887, 34.117, 151.840, 133.375, 133.377, 130.582, 133.377, 133.375
H shifts for isomer 0: 
1.376, 1.160, 1.160, 2.714, 2.714, 7.417, 7.515, 7.415, 7.515, 7.417

Reading experimental NMR data...
[PosixPath('exper/test/Proton'), PosixPath('exper/test/Carbon')]
Processing Proton Spectrum
minimisation time = 0.631831963857015 mins
     number of protons = 10
==============================
*** Open Babel Error  in ReadFile
  Cannot read from Smiles_Mol_0_0
     number of labile protons = 0
the best fit number of protons is 10
/scratch/project_2003067/DP5/DP5/Proton_processing.py:1563: VisibleDeprecationWarning: Creating an ndarray from ragged nested sequences (which is a list-or-tuple of lists-or-tuples-or ndarrays with 
different lengths or shapes) is deprecated. If you meant to do this, you must specify 'dtype=object' when creating the ndarray.
  whdel = np.where(picked_peaks == peaks_to_remove)
/scratch/project_2003067/DP5/DP5_env/lib/python3.9/site-packages/numpy/lib/function_base.py:4454: VisibleDeprecationWarning: Creating an ndarray from ragged nested sequences (which is a list-or-tupl
e of lists-or-tuples-or ndarrays with different lengths or shapes) is deprecated. If you meant to do this, you must specify 'dtype=object' when creating the ndarray.
  arr = asarray(arr)
Processing Carbon Spectrum
/scratch/project_2003067/DP5/DP5_env/lib/python3.9/site-packages/scipy/stats/_continuous_distns.py:366: RuntimeWarning: Mean of empty slice.
  loc = data.mean()
/scratch/project_2003067/DP5/DP5_env/lib/python3.9/site-packages/numpy/core/_methods.py:189: RuntimeWarning: invalid value encountered in double_scalars
  ret = ret.dtype.type(ret / rcount)
/scratch/project_2003067/DP5/DP5_env/lib/python3.9/site-packages/scipy/stats/_continuous_distns.py:371: RuntimeWarning: Mean of empty slice.
  scale = np.sqrt(((data - loc)**2).mean())
/scratch/project_2003067/DP5/DP5_env/lib/python3.9/site-packages/scipy/interpolate/fitpack2.py:667: ComplexWarning: Casting complex values to real discards the imaginary part
  self._data = dfitpack.fpcurf0(x, y, k, w=w, xb=bbox[0],

Assigning proton spectrum...

Plotting proton spectrum...

Assigning carbon spectrum...

Plotting carbon spectrum...

Calculating DP5 probabilities...
Smiles_Mol_0_0

Solvent = chloroform
Force Field = mmff

DFT optimisation Functional = b3lyp
DFT optimisation Basis = 6-31g(d,p)
DFT energy Functional = m062x
DFT energy Basis = def2tzvp
DFT NMR Functional = mPW1PW91
DFT NMR Basis = 6-311g(d)

Number of isomers = 1
Number of conformers for isomer 1 = 1

Assigned C shifts for isomer 1: 
label, calc, corrected, exp, error,prob
C1      20.89  15.80  15.60  -0.20   0.60
C2      34.12  28.96  28.88  -0.09   0.61
C6     130.58 124.91 125.57   0.66   0.62
C4     133.38 127.69 127.83   0.14   0.54
C8     133.38 127.69 127.83   0.14   0.61
C5     133.38 127.69 128.29   0.59   0.69
C7     133.38 127.69 128.29   0.59   0.70
C3     151.84 146.06 144.21  -1.84   0.27

Results of DP5 using Carbon: 
Isomer 1: 71.6%
Multiple structures required for DP4 probability calculations...

PyDP4 process completed successfully.

Traceback (most recent call last):
  File "/scratch/project_2003067/DP5/DP5/PyDP4.py", line 841, in <module>
    main(settings)
  File "/scratch/project_2003067/DP5/DP5/PyDP4.py", line 542, in main
    return NMRData, Isomers, settings, DP4data, DP5data
UnboundLocalError: local variable 'DP4data' referenced before assignment

[HowarthA]

This is not an issue with the software, PyDP4 is saying exactly why the it has exited. if you submit the workflow option s PyDP4 tries to calculate DP4 probabilities. To calculate DP4 probabilities you need to submit more than one structure as this metric is comparative. If you submit one structure and ask for DP4 probability the program will quit. DP5 is not comparative and can complete calculation on one structure, which is exactly what has been provided here, the result 71.6% is the final DP5 probability showing that this calculation has been completed correctly.

[HowarthA]

I am closing this issue as this calculation has clearly completed correctly.