ReactionMechanismGenerator
Updating to 6.6.0 XTB
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
I witnessed the same thing. xTB changed its parser since version 6.5.0 and no longer supported reading the SDF written by RDKit. I currently have to stick to version 6.4.0 for my other application. In meantime, we should probably raise an issue in RDKit, letting them write redundant zeros, or an issue in xTB to let them able to parse .sdf files from RDKit
Although, if we did raise an issue with RDKit and assuming they fixed the issue, this would not affect us correct? As we do not use the latest version of RDKit. Maybe this was already solved in an RDKit version?