ReactionMechanismGenerator / ReactionMechanismGenerator/ARC
Updating to 6.6.0 XTB
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Description
Currently we use xtb 6.3.3
If we are to update to 6.6.0 we need to modify our mol.sdf files into the correct format for xtb 6.6.0 to calculate and return normal termination
Here is an example mol.sdf file that works on 6.3.3
RDKit 3D
10 9 0 0 0 0 0 0 0 0999 V2000
1.1517 -0.3760 -0.5231 N 0 0 0 0 0 0 0 0 0 0 0 0
0.2893 0.4500 0.3115 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.1415 -0.0561 0.2592 C 0 0 0 0 0 0 0 0 0 0 0 0
1.1386 -1.3376 -0.1854 H 0 0 0 0 0 0 0 0 0 0 0 0
2.1151 -0.0555 -0.4352 H 0 0 0 0 0 0 0 0 0 0 0 0
0.6517 0.4342 1.3447 H 0 0 0 0 0 0 0 0 0 0 0 0
0.3279 1.4855 -0.0414 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.2133 -1.0839 0.6308 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.7870 0.5726 0.8809 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.5327 -0.0332 -0.7636 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
1 4 1 0
1 5 1 0
2 3 1 0
2 6 1 0
2 7 1 0
3 8 1 0
3 9 1 0
3 10 1 0
M END
$$$$
However, this will not run on xtb 6.6.0
########################################################################
[ERROR] Program stopped due to fatal error
-2- reading geometry input 'mol.sdf' failed
-1- Error: Cannot read topology from connection table
--> mol.sdf:15:13-15
|
15 | 1 2 1 0
| ^^^ unexpected value
|
########################################################################
abnormal termination of xtb
ERROR STOP
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First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Locate the code that generates the mol.sdf input and reproduce the reported failure with xtb 6.6.0. Compare the generated connection table with the format accepted by that version; done when the calculation reaches normal termination while preserving compatibility with the existing workflow.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- tooling
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Quiet
- Clarity
- Mostly clear
- Newbie friendliness
- 48/100