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missing key6 during the fragment process and Explicit valence for atom # 5 N, 8 #65

@pengacid

Description

@pengacid

I am a newcomer to the AMOEBA team and Poltype2 project, and I have encountered some unresolved issues. The problem occurred in the fragment steps, and specific errors can be found in the log text below. Thank you all.

/home/amoeba/poltype2/PoltypeModules/torsiondatabaseparser.py:3125: UserWarning: # Missing vdw parameters
warnings.warn(transferinfoline)
/home/lzp/amoeba/poltype2/PoltypeModules/torsiondatabaseparser.py:3125: UserWarning: # WARNING DEFAULT MM3 OPBEND VALUES USED
warnings.warn(transferinfoline)
[12:33:58] Explicit valence for atom # 5 N, 8, is greater than permitted
Traceback (most recent call last):
File "/home/lzp/amoeba/poltype2/PoltypeModules/lTorsionFragmentPostProcessing.py", line 418, in
Chem.SanitizeMol(mol2)
rdkit.Chem.rdchem.AtomValenceException: Explicit valence for atom # 5 N, 8, is greater than permitted
TOR [1, 5, 16, 19]
TOR [5, 16, 19, 20]
TOR [16, 19, 20, 21]
TOR [22, 21, 24, 25]
Traceback (most recent call last):
File "/home/amoeba/3f2/../poltype2/PoltypeModules/poltype.py", line 8230, in RunPoltype
poltype.main()
File "/home/amoeba/3f2/../poltype2/PoltypeModules/poltype.py", line 3655, in main
params= self.GenerateParameters()
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/amoeba/3f2/../poltype2/PoltypeModules/poltype.py", line 5129, 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 "/home/amoeba/poltype2/PoltypeModules/fragmenter.py", line 324, in GrabVdwAndTorsionParametersFromFragments
raise ValueError('Fragment job did not finish '+filename)
ValueError: Fragment job did not finish 5_16_Index_0.mol
Traceback (most recent call last):
File "/home/amoeba/3f2/../poltype2/PoltypeModules/poltype.py", line 8230, in RunPoltype
poltype.main()
File "/home/amoeba/3f2/../poltype2/PoltypeModules/poltype.py", line 3655, in main
params= self.GenerateParameters()
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/amoeba/3f2/../poltype2/PoltypeModules/poltype.py", line 5129, 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 "/home/amoeba/poltype2/PoltypeModules/fragmenter.py", line 324, in GrabVdwAndTorsionParametersFromFragments
raise ValueError('Fragment job did not finish '+filename)
ValueError: Fragment job did not finish 5_16_Index_0.mol

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/home/amoeba/3f2/../poltype2/PoltypeModules/poltype.py", line 8254, in
RunPoltype()
File "/home/amoeba/3f2/../poltype2/PoltypeModules/poltype.py", line 8253, 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!

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