# Regarding the pmx tutorial

**URL:** <https://ask.bioexcel.eu/t/regarding-the-pmx-tutorial/5356>\
**Category:** Uncategorized\
**Tags:** support\
**Created:** [December 5, 2024, 7:00am UTC](https://ask.bioexcel.eu/t/regarding-the-pmx-tutorial/5356 "2024-12-05T07:00:44Z")\
**Posts on this page:** 1\
**Page:** 1

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**Author:** ![jinurajkr](https://avatars.discourse-cdn.com/v4/letter/j/d26b3c/32.png) [@jinurajkr](https://ask.bioexcel.eu/u/jinurajkr)\
**Post date:** [December 5, 2024, 7:00am UTC](https://ask.bioexcel.eu/t/regarding-the-pmx-tutorial/5356/1 "2024-12-05T07:00:44Z")

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Dear Team pmx  
I was trying to follow the tutorial from pmx given in the following link:  
[http://pmx.mpibpc.mpg.de/Old\_Tutorials/janssen\_tutorial\_ligand/index.html](http://pmx.mpibpc.mpg.de/Old_Tutorials/janssen_tutorial_ligand/index.html)  
The process followed:   
The lig\_1a and lig\_5 were downloaded from the above page, unzipped and kept in a folder. Then:

1. The first step is to merge both ffMOL.itp files into one. I was able to run the script one\_ff\_file.py using the following command.  
python one\_ff\_file.py -ffitp lig\_1a/ffMOL.itp lig\_5/ffMOL.itp -ffitp\_out ffMOL.itp  
Running the above command successfully generated ffMOL.itp
2. The second step, atom mapping has to be done using the script atoms\_to\_morph.py using the following command.  
python atoms\_to\_morph.py -i1 lig\_1a/lig\_1a.pdb -i2 lig\_5/lig\_5.pdb -o pairs.dat - alignment -H2H  
The above step was done by activating the pmx environment as indicated by the instructions. . Initially there were some some warning on indentation errors. Cleared those issues, and I was able to run the script without error/warning.  
Now the problem is I was unable to find the output files in the working folder. How to resolve it? I observe that in def main() in script atom\_to\_morph.py there is no commands invoked. Please let me know if I have to tweak this.

Thanks, and regards