# Error with pmx and openforcefield generated files

**URL:** <https://ask.bioexcel.eu/t/error-with-pmx-and-openforcefield-generated-files/5402>\
**Category:** pmx\
**Created:** [January 25, 2025, 6:54pm UTC](https://ask.bioexcel.eu/t/error-with-pmx-and-openforcefield-generated-files/5402 "2025-01-25T18:54:30Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![lwhitm1](https://avatars.discourse-cdn.com/v4/letter/l/958977/32.png) [@lwhitm1](https://ask.bioexcel.eu/u/lwhitm1)\
**Post date:** [January 25, 2025, 6:54pm UTC](https://ask.bioexcel.eu/t/error-with-pmx-and-openforcefield-generated-files/5402/1 "2025-01-25T18:54:30Z")

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I have attempted to use openff-toolkit generate files as inputs for the ligand\_tutorial. The atomMapping finished without error, but, during the makeHybrid component, I get this error in my log file:  
"  
ligandHybridTop\_\_log\_\> Constructing dummies…  
ligandHybridTop\_\_log\_\> Dummies in stateA:  
ligandHybridTop\_\_log\_\> Dummy…: 51 DUM\_MOL0\_24 | 0.00 | 12.01 → MOL0\_24 | -0.18 | 12.01  
ligandHybridTop\_\_log\_\> Dummy…: 52 DUM\_MOL0\_27 | 0.00 | 12.01 → MOL0\_27 | 0.11 | 12.01  
ligandHybridTop\_\_log\_\> Dummy…: 53 DUM\_MOL0\_51 | 0.00 | 1.01 → MOL0\_51 | 0.05 | 1.01  
ligandHybridTop\_\_log\_\> Dummy…: 54 DUM\_MOL0\_52 | 0.00 | 1.01 → MOL0\_52 | 0.05 | 1.01  
ligandHybridTop\_\_log\_\> Dummy…: 55 DUM\_MOL0\_53 | 0.00 | 1.01 → MOL0\_53 | 0.05 | 1.01  
ligandHybridTop\_\_log\_\> Dummies in stateB:  
ligandHybridTop\_\_log\_\> Dummy…: 48 MOL0\_47 | 0.13 | 1.01 → DUM\_MOL0\_47 | 0.00 | 1.01  
ligandHybridTop\_\_log\_\> Construct bonds…  
ligandHybridTop\_\_log\_\> Error: Something went wrong while assigning bonds!  
ligandHybridTop\_\_log\_\> A-\> Atom1: 1-N Atom2: 27-H  
ligandHybridTop\_\_log\_\> B-\> Atom1: 1-N Atom2: 37-H  
ligandHybridTop\_\_log\_\> Exiting…  
"  
I am not sure why the error is occuring as openff bond parameters are explicitly stated in the files. It will not allow me to attach the files, but I have uploaded them here: [pmx\_openff](https://o365coloradoedu-my.sharepoint.com/:f:/g/personal/liwh2139_colorado_edu/EpVk0wUz_ZJImXqxhjcnzWIBkpWhpcZlXhNrjUIU8X0lxA?e=F8ntNz)

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**Author:** ![Sudchem](https://avatars.discourse-cdn.com/v4/letter/s/ecccb3/32.png) [@Sudchem](https://ask.bioexcel.eu/u/Sudchem)\
**Post date:** [January 27, 2025, 11:46am UTC](https://ask.bioexcel.eu/t/error-with-pmx-and-openforcefield-generated-files/5402/2 "2025-01-27T11:46:05Z")

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Hi,  
The error likely arises because the atom ordering (indexing) in the itp file (MOL.itp) doesn’t match with the pdb file (mol\_gmx.pdb).

Reordering the atoms in pdb file with proper indexing to match the itp will likely resolve the issue.

All the best.