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

[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!

[leucinw]

As indicated the error is due to that the Nitrogen atom has 8 explicit valence.
It will be better for me to look into the issue if you could provide the parent molecule sdf file and 5_16_Index_0.mol that poltype generated.

[pengacid]

As indicated the error is due to that the Nitrogen atom has 8 explicit valence. It will be better for me to look into the issue if you could provide the parent molecule sdf file and 5_16_Index_0.mol that poltype generated.

Thank you for your reply. I have attached the sdf file of the entire molecule and the 5_16_idex_0.mol generated by poltype. It is worth mentioning that there is no nitrogen atom in this mol file.
sdf_5_16_Index_0.zip

[Yunhao-Mei]

I have encountered the exactly same problem. The exception message was rdkit.Chem.rdchem.AtomValenceException: Explicit valence for atom # 0 P, 6, is greater than permitted, but there is no phosphorus in my molecule.

Btw I have tried to fix this issue by myself, but torsiondatabaseparser.py is terribly organized without any comments.

[leucinw]

Hi @Yunhao-Mei and @pengacid , one Poltype user identified the issue you saw. This was actually due to the RDKit version you guys are using. Please try 2024.3.6 (or older) version of RDKit and re-run your poltype job.

[pengacid]

Hi @Yunhao-Mei and @pengacid , one Poltype user identified the issue you saw. This was actually due to the RDKit version you guys are using. Please try 2024.3.6 (or older) version of RDKit and re-run your poltype job.

This error still exists. My computer's RDKit version was 2024.3. I tried 2023.09, but still got this error.