Missing discrete file

[chesnut0701-star]

Hello, I tried to run the godmd run on my computer, then I get the error message like this:
2025-10-01 14:19:49,096 [MainThread ] [INFO ] Exit code: 127
2025-10-01 14:19:49,096 [MainThread ] [INFO ] /bin/bash: line 1: discrete: command not found

I am still new to this field, did I miss anything? Thank you

[adamhospital]

Hi there!
Can I ask you how did you installed the biobb_godmd package?
If installed using pip, the software dependencies are ignored (only Python libraries are installed).
We recommend using Conda to avoid this problem.
"discrete" is the (binary) software that actually computes the conformational transition.
If you follow the instructions that you can find here you should be able to run the demonstration workflow using GOdMD.
Hope it helps!

[chesnut0701-star]

Hei, thank you for your reply. Yes, I have installed GodMD via conda, and followed the workflow, but another error message occured: *Fortran runtime error: Missing comma between descriptors(" |Min time to eq. energy(ps) |Ener_evo_size |"I5" |")* ^. I recomplied the main.F, added the comma, now it is working :) I am not sure if it was only me, maybe you want to double check it. Thank you so much for your help :) My name is Li, I am from biocomputing group at the University of Oulu, Finland. If you ever come to Oulu, please let me know :) Best wishes, Li to 2.10.2025 klo 10.42 Adam Hospital Gasch ***@***.***) kirjoitti:

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*adamhospital* left a comment (bioexcel/biobb_godmd#1) <#1 (comment)> Hi there! Can I ask you how did you installed the biobb_godmd package? If installed using pip, the software dependencies are ignored (only Python libraries are installed). We recommend using Conda to avoid this problem. "*discrete*" is the (binary) software that actually computes the conformational transition. If you follow the instructions that you can find here <https://github.com/bioexcel/biobb_wf_godmd> you should be able to run the demonstration workflow using GOdMD. Hope it helps! — Reply to this email directly, view it on GitHub <#1 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/BYEW4XLAX36SYYKJHVAV2RD3VTJQBAVCNFSM6AAAAACH75G6IKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZTGNJZGY2DSMRSHE> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[RubenChM]

Thanks for reporting the issue!

For some reason this problems was not showing in the CI tests but I could reproduce it locally, even though both are using the same compiled program.

In any case, I fixed the source with the change you mentioned and now the 5.1.2 version comes with it so you do not have to compile it yourself.