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Getting Error while running poltype2
Hi, I am getting the following error while running poltype.py. Could you please help me to fix the issue. Also it is using psi4 how can use gaussian instead.
/storage/nas_scr/shared/groups/valsson/Pradip_Runs/AMOEBA_test/master/PoltypeModules/poltype.py:3307: SyntaxWarning: invalid escape sequence '\s'
patt_list.append(('psi4', 'header', re.compile('^\s+Psi4\: An Open-Source Ab Initio Electronic Structure Package')))
/storage/nas_scr/shared/groups/valsson/Pradip_Runs/AMOEBA_test/master/PoltypeModules/poltype.py:3308: SyntaxWarning: invalid escape sequence '\s'
patt_list.append(('psi4', 'date', re.compile('^\s+Psi4 (started|stopped) on: ')))
/storage/nas_scr/shared/groups/valsson/Pradip_Runs/AMOEBA_test/master/PoltypeModules/poltype.py:3309: SyntaxWarning: invalid escape sequence '\*'
patt_list.append(('psi4', 'tstart', re.compile('^\*\*\* (tstart|tstop)\(\) called on')))
/storage/nas_scr/shared/groups/valsson/Pradip_Runs/AMOEBA_test/master/PoltypeModules/poltype.py:3310: SyntaxWarning: invalid escape sequence '\s'
patt_list.append(('psi4', 'time', re.compile('^\s+total time =\s+\S+ seconds =\s+\S+ minutes')))
/storage/nas_scr/shared/groups/valsson/Pradip_Runs/AMOEBA_test/master/PoltypeModules/poltype.py:3311: SyntaxWarning: invalid escape sequence '\s'
patt_list.append(('psi4', 'basis', re.compile('^\s+=> Loading Basis Set <=')))
/storage/nas_scr/shared/groups/valsson/Pradip_Runs/AMOEBA_test/master/PoltypeModules/poltype.py:3312: SyntaxWarning: invalid escape sequence '\*'
patt_list.append(('psi4', 'normal_term', re.compile('^\*\*\* Psi4 exiting successfully.')))
/storage/nas_scr/shared/groups/valsson/Pradip_Runs/AMOEBA_test/master/PoltypeModules/poltype.py:3313: SyntaxWarning: invalid escape sequence '\*'
patt_list.append(('psi4', 'error_term', re.compile('^\*\*\* Psi4 encountered an error.')))
/storage/nas_scr/shared/groups/valsson/Pradip_Runs/AMOEBA_test/master/PoltypeModules/poltype.py:3338: SyntaxWarning: invalid escape sequence '\*'
patt_map['psi4'].append(('normal_term', True, re.compile('^\*\*\* Psi4 exiting successfully.')))
/storage/nas_scr/shared/groups/valsson/Pradip_Runs/AMOEBA_test/master/PoltypeModules/poltype.py:3339: SyntaxWarning: invalid escape sequence '\*'
patt_map['psi4'].append(('error_term', True, re.compile('^\*\*\* Psi4 encountered an error.')))
/storage/nas_scr/shared/groups/valsson/Pradip_Runs/AMOEBA_test/master/PoltypeModules/poltype.py:3340: SyntaxWarning: invalid escape sequence '\('
patt_map['psi4'].append(('error_term', True, re.compile('^Traceback \(most recent call last\):')))
/storage/nas_scr/shared/groups/valsson/Pradip_Runs/AMOEBA_test/master/PoltypeModules/poltype.py:3341: SyntaxWarning: invalid escape sequence '\s'
patt_map['psi4'].append(('opt', 'error', re.compile('(^\s+Optimization failed to converge!\s+~|Could not converge geometry optimization in \d+ iterations.)')))
/storage/nas_scr/shared/groups/valsson/Pradip_Runs/AMOEBA_test/master/PoltypeModules/poltype.py:3342: SyntaxWarning: invalid escape sequence '\s'
patt_map['psi4'].append(('opt', 'success', re.compile('(^\s+Optimization converged!\s+~|^\s+Final optimized geometry)')))
WARNING:pymbar.timeseries:Warning on use of the timeseries module: If the inherent timescales of the system are long compared to those being analyzed, this statistical inefficiency may be an underestimate. The estimate presumes the use of many statistically independent samples. Tests should be performed to assess whether this condition is satisfied. Be cautious in the interpretation of the data.
WARNING:pymbar.mbar_solvers:
****** PyMBAR will use 64-bit JAX! *******
* JAX is currently set to 32-bit bitsize *
* which is its default. *
* *
* PyMBAR requires 64-bit mode and WILL *
* enable JAX's 64-bit mode when called. *
* *
* This MAY cause problems with other *
* Uses of JAX in the same code. *
******************************************
INFO:pymbar.mbar_solvers:JAX detected. Using JAX acceleration.
Poltype -- Polarizable atom typer of small molecules for the AMOEBA polarizable force field
Please cite:
Wu, J.C.; Chattree, G.; Ren, P.Y.; Automation of AMOEBA polarizable force field
parameterization for small molecules. Theor Chem Acc.
Version 2.3.1 May 2021
Copyright (c) Johnny Wu, Gaurav Chattree, Brandon Walker, Matthew Harger and Pengyu Ren 2019
All Rights Reserved
##############################################################################################################
Calling: analyze /storage/nas_scr/shared/groups/valsson/Pradip_Runs/AMOEBA_test/master/VersionFiles/water.xyz -k /storage/nas_scr/shared/groups/valsson/Pradip_Runs/AMOEBA_test/master/VersionFiles/water.key e> version.out
==============================
*** Open Babel Error in LoadFragments
Cannot open ring-fragments-index.txt
==============================
*** Open Babel Error in ParseParamFile
Cannot open parameter file
==============================
*** Open Babel Error in ParseParamFile
Cannot open UFF.prm
==============================
*** Open Babel Error in SetTypes
Cannot open UFF.prm
1 molecule converted
Converting water_3D.mol to 3D
==============================
*** Open Babel Error in LoadFragments
Cannot open ring-fragments-index.txt
==============================
*** Open Babel Error in ParseParamFile
Cannot open parameter file
==============================
*** Open Babel Error in ParseParamFile
Cannot open UFF.prm
==============================
*** Open Babel Error in SetTypes
Cannot open UFF.prm
1 molecule converted
Converting conftest.mol to 3D
For help, use: python dimorphite_dl.py --help
If you use Dimorphite-DL in your research, please cite:
Ropp PJ, Kaminsky JC, Yablonski S, Durrant JD (2019) Dimorphite-DL: An
open-source program for enumerating the ionization states of drug-like small
molecules. J Cheminform 11:14. doi:10.1186/s13321-019-0336-9.
Traceback (most recent call last):
File "/storage/nas_scr/shared/groups/valsson/Pradip_Runs/AMOEBA_test/master/PoltypeModules/poltype.py", line 8197, in RunPoltype
poltype.main()
File "/storage/nas_scr/shared/groups/valsson/Pradip_Runs/AMOEBA_test/master/PoltypeModules/poltype.py", line 3649, in main
params= self.GenerateParameters()
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/storage/nas_scr/shared/groups/valsson/Pradip_Runs/AMOEBA_test/master/PoltypeModules/poltype.py", line 5177, in GenerateParameters
lmodifytinkerkey.mod_final_key(self)
File "/storage/nas_scr/shared/groups/valsson/Pradip_Runs/AMOEBA_test/master/PoltypeModules/lmodifytinkerkey.py", line 527, in mod_final_key
for mol in pybel.readfile(inpformat,inpfile):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/ps0579/.conda/envs/poltype2/lib/python3.12/site-packages/openbabel/pybel.py", line 161, in readfile
raise IOError("No such file: '%s'" % filename)
OSError: No such file: 'water_3D.mol'
Traceback (most recent call last):
File "/storage/nas_scr/shared/groups/valsson/Pradip_Runs/AMOEBA_test/master/PoltypeModules/poltype.py", line 8197, in RunPoltype
poltype.main()
File "/storage/nas_scr/shared/groups/valsson/Pradip_Runs/AMOEBA_test/master/PoltypeModules/poltype.py", line 3649, in main
params= self.GenerateParameters()
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/storage/nas_scr/shared/groups/valsson/Pradip_Runs/AMOEBA_test/master/PoltypeModules/poltype.py", line 5177, in GenerateParameters
lmodifytinkerkey.mod_final_key(self)
File "/storage/nas_scr/shared/groups/valsson/Pradip_Runs/AMOEBA_test/master/PoltypeModules/lmodifytinkerkey.py", line 527, in mod_final_key
for mol in pybel.readfile(inpformat,inpfile):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/ps0579/.conda/envs/poltype2/lib/python3.12/site-packages/openbabel/pybel.py", line 161, in readfile
raise IOError("No such file: '%s'" % filename)
OSError: No such file: 'water_3D.mol'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/storage/nas_scr/shared/groups/valsson/Pradip_Runs/AMOEBA_test/master/PoltypeModules/poltype.py", line 8221, in <module>
RunPoltype()
File "/storage/nas_scr/shared/groups/valsson/Pradip_Runs/AMOEBA_test/master/PoltypeModules/poltype.py", line 8220, in RunPoltype
raise ValueError('Houston, we have a problem. Buy a developer some coffee!')
ValueError: Houston, we have a problem. Buy a developer some coffee!
The error is due to openbabel could not find force field parameters when doing gen3d conversion. Please check openbabel for solutions. If you want to use gaussian, simply add use_gaus in poltype.ini file. Make sure g09 or g16 is in your $PATH.
I have figured out the open babel issue. Bust still getting the error like,
/storage/nas_scr/shared/groups/valsson/Pradip_Runs/AMOEBA_test/master/PoltypeModules/poltype.py:3307: SyntaxWarning: invalid escape sequence '\s'
patt_list.append(('psi4', 'header', re.compile('^\s+Psi4\: An Open-Source Ab Initio Electronic Structure Package')))
/storage/nas_scr/shared/groups/valsson/Pradip_Runs/AMOEBA_test/master/PoltypeModules/poltype.py:3308: SyntaxWarning: invalid escape sequence '\s'
patt_list.append(('psi4', 'date', re.compile('^\s+Psi4 (started|stopped) on: ')))
/storage/nas_scr/shared/groups/valsson/Pradip_Runs/AMOEBA_test/master/PoltypeModules/poltype.py:3309: SyntaxWarning: invalid escape sequence '\*'
patt_list.append(('psi4', 'tstart', re.compile('^\*\*\* (tstart|tstop)\(\) called on')))
/storage/nas_scr/shared/groups/valsson/Pradip_Runs/AMOEBA_test/master/PoltypeModules/poltype.py:3310: SyntaxWarning: invalid escape sequence '\s'
patt_list.append(('psi4', 'time', re.compile('^\s+total time =\s+\S+ seconds =\s+\S+ minutes')))
/storage/nas_scr/shared/groups/valsson/Pradip_Runs/AMOEBA_test/master/PoltypeModules/poltype.py:3311: SyntaxWarning: invalid escape sequence '\s'
patt_list.append(('psi4', 'basis', re.compile('^\s+=> Loading Basis Set <=')))
/storage/nas_scr/shared/groups/valsson/Pradip_Runs/AMOEBA_test/master/PoltypeModules/poltype.py:3312: SyntaxWarning: invalid escape sequence '\*'
patt_list.append(('psi4', 'normal_term', re.compile('^\*\*\* Psi4 exiting successfully.')))
/storage/nas_scr/shared/groups/valsson/Pradip_Runs/AMOEBA_test/master/PoltypeModules/poltype.py:3313: SyntaxWarning: invalid escape sequence '\*'
patt_list.append(('psi4', 'error_term', re.compile('^\*\*\* Psi4 encountered an error.')))
/storage/nas_scr/shared/groups/valsson/Pradip_Runs/AMOEBA_test/master/PoltypeModules/poltype.py:3338: SyntaxWarning: invalid escape sequence '\*'
patt_map['psi4'].append(('normal_term', True, re.compile('^\*\*\* Psi4 exiting successfully.')))
/storage/nas_scr/shared/groups/valsson/Pradip_Runs/AMOEBA_test/master/PoltypeModules/poltype.py:3339: SyntaxWarning: invalid escape sequence '\*'
patt_map['psi4'].append(('error_term', True, re.compile('^\*\*\* Psi4 encountered an error.')))
/storage/nas_scr/shared/groups/valsson/Pradip_Runs/AMOEBA_test/master/PoltypeModules/poltype.py:3340: SyntaxWarning: invalid escape sequence '\('
patt_map['psi4'].append(('error_term', True, re.compile('^Traceback \(most recent call last\):')))
/storage/nas_scr/shared/groups/valsson/Pradip_Runs/AMOEBA_test/master/PoltypeModules/poltype.py:3341: SyntaxWarning: invalid escape sequence '\s'
patt_map['psi4'].append(('opt', 'error', re.compile('(^\s+Optimization failed to converge!\s+~|Could not converge geometry optimization in \d+ iterations.)')))
/storage/nas_scr/shared/groups/valsson/Pradip_Runs/AMOEBA_test/master/PoltypeModules/poltype.py:3342: SyntaxWarning: invalid escape sequence '\s'
patt_map['psi4'].append(('opt', 'success', re.compile('(^\s+Optimization converged!\s+~|^\s+Final optimized geometry)')))
WARNING:pymbar.timeseries:Warning on use of the timeseries module: If the inherent timescales of the system are long compared to those being analyzed, this statistical inefficiency may be an underestimate. The estimate presumes the use of many statistically independent samples. Tests should be performed to assess whether this condition is satisfied. Be cautious in the interpretation of the data.
WARNING:pymbar.mbar_solvers:
****** PyMBAR will use 64-bit JAX! *******
* JAX is currently set to 32-bit bitsize *
* which is its default. *
* *
* PyMBAR requires 64-bit mode and WILL *
* enable JAX's 64-bit mode when called. *
* *
* This MAY cause problems with other *
* Uses of JAX in the same code. *
******************************************
INFO:pymbar.mbar_solvers:JAX detected. Using JAX acceleration.
Poltype -- Polarizable atom typer of small molecules for the AMOEBA polarizable force field
Please cite:
Wu, J.C.; Chattree, G.; Ren, P.Y.; Automation of AMOEBA polarizable force field
parameterization for small molecules. Theor Chem Acc.
Version 2.3.1 May 2021
Copyright (c) Johnny Wu, Gaurav Chattree, Brandon Walker, Matthew Harger and Pengyu Ren 2019
All Rights Reserved
##############################################################################################################
Calling: analyze /storage/nas_scr/shared/groups/valsson/Pradip_Runs/AMOEBA_test/master/VersionFiles/water.xyz -k /storage/nas_scr/shared/groups/valsson/Pradip_Runs/AMOEBA_test/master/VersionFiles/water.key e> version.out
1 molecule converted
Converting water_3D.mol to 3D
1 molecule converted
Converting conftest.mol to 3D
For help, use: python dimorphite_dl.py --help
If you use Dimorphite-DL in your research, please cite:
Ropp PJ, Kaminsky JC, Yablonski S, Durrant JD (2019) Dimorphite-DL: An
open-source program for enumerating the ionization states of drug-like small
molecules. J Cheminform 11:14. doi:10.1186/s13321-019-0336-9.
Searching SMARTS database: 0it [00:00, ?it/s]
Searching SMARTS database: 0it [00:00, ?it/s]
Searching SMARTS database: 0it [00:00, ?it/s]
Searching SMARTS database: 0it [00:00, ?it/s]
Searching SMARTS database: 0it [00:00, ?it/s]
Searching SMARTS database: 0it [00:00, ?it/s]
Searching SMARTS database: 0it [00:00, ?it/s]
amoeba09 search for [0]: 100%|████████████████████████████████████████████████████████████████████| 57/57 [00:00<00:00, 12246.46it/s]
amoeba09 search for [1]: 100%|█████████████████████████████████████████████████████████████████████| 57/57 [00:00<00:00, 7430.93it/s]
amoeba09 search for [2]: 100%|█████████████████████████████████████████████████████████████████████| 57/57 [00:00<00:00, 7174.27it/s]
amoeba09 search for [1, 0]: 100%|█████████████████████████████████████████████████████████████████| 57/57 [00:00<00:00, 52998.30it/s]
amoeba09 search for [2, 0]: 100%|█████████████████████████████████████████████████████████████████| 57/57 [00:00<00:00, 52417.30it/s]
amoeba09 search for [2, 0, 1]: 100%|█████████████████████████████████████████████████████████████| 57/57 [00:00<00:00, 249296.48it/s]
amoeba09 search for [2, 0, 1]: 100%|█████████████████████████████████████████████████████████████| 57/57 [00:00<00:00, 242469.91it/s]
Traceback (most recent call last):
File "/storage/nas_scr/shared/groups/valsson/Pradip_Runs/AMOEBA_test/master/PoltypeModules/poltype.py", line 8197, in RunPoltype
poltype.main()
File "/storage/nas_scr/shared/groups/valsson/Pradip_Runs/AMOEBA_test/master/PoltypeModules/poltype.py", line 3649, in main
params= self.GenerateParameters()
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/storage/nas_scr/shared/groups/valsson/Pradip_Runs/AMOEBA_test/master/PoltypeModules/poltype.py", line 5177, in GenerateParameters
lmodifytinkerkey.mod_final_key(self)
File "/storage/nas_scr/shared/groups/valsson/Pradip_Runs/AMOEBA_test/master/PoltypeModules/lmodifytinkerkey.py", line 527, in mod_final_key
for mol in pybel.readfile(inpformat,inpfile):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/ps0579/.conda/envs/poltype2/lib/python3.12/site-packages/openbabel/pybel.py", line 161, in readfile
raise IOError("No such file: '%s'" % filename)
OSError: No such file: 'water_3D.mol'
Traceback (most recent call last):
File "/storage/nas_scr/shared/groups/valsson/Pradip_Runs/AMOEBA_test/master/PoltypeModules/poltype.py", line 8197, in RunPoltype
poltype.main()
File "/storage/nas_scr/shared/groups/valsson/Pradip_Runs/AMOEBA_test/master/PoltypeModules/poltype.py", line 3649, in main
params= self.GenerateParameters()
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/storage/nas_scr/shared/groups/valsson/Pradip_Runs/AMOEBA_test/master/PoltypeModules/poltype.py", line 5177, in GenerateParameters
lmodifytinkerkey.mod_final_key(self)
File "/storage/nas_scr/shared/groups/valsson/Pradip_Runs/AMOEBA_test/master/PoltypeModules/lmodifytinkerkey.py", line 527, in mod_final_key
for mol in pybel.readfile(inpformat,inpfile):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/ps0579/.conda/envs/poltype2/lib/python3.12/site-packages/openbabel/pybel.py", line 161, in readfile
raise IOError("No such file: '%s'" % filename)
OSError: No such file: 'water_3D.mol'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/storage/nas_scr/shared/groups/valsson/Pradip_Runs/AMOEBA_test/master/PoltypeModules/poltype.py", line 8221, in <module>
RunPoltype()
File "/storage/nas_scr/shared/groups/valsson/Pradip_Runs/AMOEBA_test/master/PoltypeModules/poltype.py", line 8220, in RunPoltype
raise ValueError('Houston, we have a problem. Buy a developer some coffee!')
ValueError: Houston, we have a problem. Buy a developer some coffee!
to use Gaussian are you saying this,
structure=water.sdf
use_gaus
where can I find the input option for the poltype.ini file?
Fixed in this commit 055bd91021f895a4eef0db9dcd1503de49bed9c1 For the keywords, please refer to here.
Hi, I am doing a poltype calculation for this molecule. I am getting some errors which I couldn't understand much.
==============================
*** Open Babel Warning in ReadMolecule
Failed to kekulize aromatic bonds in MOL file
Traceback (most recent call last):
File "/storage/nas_scr/shared/groups/valsson/Pradip_Runs/AMOEBA_test/master/PoltypeModules/poltype.py", line 8203, in RunPoltype
poltype.main()
File "/storage/nas_scr/shared/groups/valsson/Pradip_Runs/AMOEBA_test/master/PoltypeModules/poltype.py", line 3655, in main
params= self.GenerateParameters()
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/storage/nas_scr/shared/groups/valsson/Pradip_Runs/AMOEBA_test/master/PoltypeModules/poltype.py", line 4816, in GenerateParameters
raise ValueError('Bond created after optimization !'+str(bond))
ValueError: Bond created after optimization ![18, 4]
Traceback (most recent call last):
File "/storage/nas_scr/shared/groups/valsson/Pradip_Runs/AMOEBA_test/master/PoltypeModules/poltype.py", line 8203, in RunPoltype
poltype.main()
File "/storage/nas_scr/shared/groups/valsson/Pradip_Runs/AMOEBA_test/master/PoltypeModules/poltype.py", line 3655, in main
params= self.GenerateParameters()
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/storage/nas_scr/shared/groups/valsson/Pradip_Runs/AMOEBA_test/master/PoltypeModules/poltype.py", line 4816, in GenerateParameters
raise ValueError('Bond created after optimization !'+str(bond))
ValueError: Bond created after optimization ![18, 4]
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/storage/nas_scr/shared/groups/valsson/Pradip_Runs/AMOEBA_test/master/PoltypeModules/poltype.py", line 8227, in <module>
RunPoltype()
File "/storage/nas_scr/shared/groups/valsson/Pradip_Runs/AMOEBA_test/master/PoltypeModules/poltype.py", line 8226, in RunPoltype
raise ValueError('Houston, we have a problem. Buy a developer some coffee!')
ValueError: Houston, we have a problem. Buy a developer some coffee!
Traceback (most recent call last):
File "/storage/nas_scr/shared/groups/valsson/Pradip_Runs/AMOEBA_test/master/PoltypeModules/poltype.py", line 8203, in RunPoltype
poltype.main()
File "/storage/nas_scr/shared/groups/valsson/Pradip_Runs/AMOEBA_test/master/PoltypeModules/poltype.py", line 3655, in main
params= self.GenerateParameters()
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/storage/nas_scr/shared/groups/valsson/Pradip_Runs/AMOEBA_test/master/PoltypeModules/poltype.py", line 5183, in GenerateParameters
lmodifytinkerkey.mod_final_key(self)
File "/storage/nas_scr/shared/groups/valsson/Pradip_Runs/AMOEBA_test/master/PoltypeModules/lmodifytinkerkey.py", line 515, in mod_final_key
atomnumbers, types = np.loadtxt(xyz, usecols=(0, 5,), unpack=True, dtype="str", skiprows=1)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/cm/shared/apps/MINICONDA/23.1.0_Py3.9/envs/poltype2/lib/python3.12/site-packages/numpy/lib/npyio.py", line 1373, in loadtxt
arr = _read(fname, dtype=dtype, comment=comment, delimiter=delimiter,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/cm/shared/apps/MINICONDA/23.1.0_Py3.9/envs/poltype2/lib/python3.12/site-packages/numpy/lib/npyio.py", line 992, in _read
fh = np.lib._datasource.open(fname, 'rt', encoding=encoding)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/cm/shared/apps/MINICONDA/23.1.0_Py3.9/envs/poltype2/lib/python3.12/site-packages/numpy/lib/_datasource.py", line 193, in open
return ds.open(path, mode, encoding=encoding, newline=newline)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/cm/shared/apps/MINICONDA/23.1.0_Py3.9/envs/poltype2/lib/python3.12/site-packages/numpy/lib/_datasource.py", line 533, in open
raise FileNotFoundError(f"{path} not found.")
FileNotFoundError: final.xyz not found.
Traceback (most recent call last):
File "/storage/nas_scr/shared/groups/valsson/Pradip_Runs/AMOEBA_test/master/PoltypeModules/poltype.py", line 8203, in RunPoltype
poltype.main()
File "/storage/nas_scr/shared/groups/valsson/Pradip_Runs/AMOEBA_test/master/PoltypeModules/poltype.py", line 3655, in main
params= self.GenerateParameters()
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/storage/nas_scr/shared/groups/valsson/Pradip_Runs/AMOEBA_test/master/PoltypeModules/poltype.py", line 5183, in GenerateParameters
lmodifytinkerkey.mod_final_key(self)
File "/storage/nas_scr/shared/groups/valsson/Pradip_Runs/AMOEBA_test/master/PoltypeModules/lmodifytinkerkey.py", line 515, in mod_final_key
atomnumbers, types = np.loadtxt(xyz, usecols=(0, 5,), unpack=True, dtype="str", skiprows=1)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/cm/shared/apps/MINICONDA/23.1.0_Py3.9/envs/poltype2/lib/python3.12/site-packages/numpy/lib/npyio.py", line 1373, in loadtxt
arr = _read(fname, dtype=dtype, comment=comment, delimiter=delimiter,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/cm/shared/apps/MINICONDA/23.1.0_Py3.9/envs/poltype2/lib/python3.12/site-packages/numpy/lib/npyio.py", line 992, in _read
fh = np.lib._datasource.open(fname, 'rt', encoding=encoding)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/cm/shared/apps/MINICONDA/23.1.0_Py3.9/envs/poltype2/lib/python3.12/site-packages/numpy/lib/_datasource.py", line 193, in open
return ds.open(path, mode, encoding=encoding, newline=newline)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/cm/shared/apps/MINICONDA/23.1.0_Py3.9/envs/poltype2/lib/python3.12/site-packages/numpy/lib/_datasource.py", line 533, in open
raise FileNotFoundError(f"{path} not found.")
FileNotFoundError: final.xyz not found.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/storage/nas_scr/shared/groups/valsson/Pradip_Runs/AMOEBA_test/master/PoltypeModules/poltype.py", line 8227, in <module>
RunPoltype()
File "/storage/nas_scr/shared/groups/valsson/Pradip_Runs/AMOEBA_test/master/PoltypeModules/poltype.py", line 8226, in RunPoltype
raise ValueError('Houston, we have a problem. Buy a developer some coffee!')
ValueError: Houston, we have a problem. Buy a developer some coffee!
File "/storage/nas_scr/shared/groups/valsson/Pradip_Runs/AMOEBA_test/master/PoltypeModules/poltype.py", line 8203, in RunPoltype
poltype.main()
File "/storage/nas_scr/shared/groups/valsson/Pradip_Runs/AMOEBA_test/master/PoltypeModules/poltype.py", line 3655, in main
params= self.GenerateParameters()
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/storage/nas_scr/shared/groups/valsson/Pradip_Runs/AMOEBA_test/master/PoltypeModules/poltype.py", line 5102, in GenerateParameters
frag.GrabVdwAndTorsionParametersFromFragments(self,rotbndindextofragmentfilepath,equivalentrotbndindexarrays,rotbndindextoringtor,self.key6fname,self.key7fname,rotbndindextoparentrotbndindexes,rotbndindextosmartsindexarray) # just dump to key_6 since does not exist for parent molecule
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/storage/nas_scr/shared/groups/valsson/Pradip_Runs/AMOEBA_test/master/PoltypeModules/fragmenter.py", line 324, in GrabVdwAndTorsionParametersFromFragments
raise ValueError('Fragment job did not finish '+filename)
ValueError: Fragment job did not finish 4_9_Index_0_GrowFragment_3.mol