# MDrun\_Cgenff\_Charmm\_error

**URL:** <https://gromacs.bioexcel.eu/t/mdrun-cgenff-charmm-error/4940>\
**Category:** User discussions\
**Tags:** mdrun\
**Created:** [October 2, 2022, 1:17pm UTC](https://gromacs.bioexcel.eu/t/mdrun-cgenff-charmm-error/4940 "2022-10-02T13:17:43Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![Rudhra](https://avatars.discourse-cdn.com/v4/letter/r/958977/32.png) [@Rudhra](https://gromacs.bioexcel.eu/u/Rudhra)\
**Post date:** [October 2, 2022, 1:17pm UTC](https://gromacs.bioexcel.eu/t/mdrun-cgenff-charmm-error/4940/1 "2022-10-02T13:17:43Z")

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GROMACS version:5.1.4  
GROMACS modification: Yes/No  
Here post your question  
Dear Sir/Ma’am,  
I want to create ligand topology file using cgenff server (Charmm force field). I downloaded the ligand str file from cgenff. Then I followed the protein- ligand complex gromacs tutorial. I got the following error (Screenshot) in itp, prm file generatio step (python cgenff\_charmm2gmx.py JZ4 jz4\_fix.mol2 jz4.str charmm36-mar2019.ff). Since I am newbie to bioinformatics, I couldnt solve this error. My python version is 3, I used the Python 3.x, NetworkX 2.3 script.  
I removed ligand name and ran the commandline with ligand\_fix\_mol2 and ligand. str file alone, I was getting another resname error. What can I do to solve this error?

 ![chaarm_error](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/2/2dbe33110643a4a0295be3712a12e5e1cec06135.png)

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**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\
**Post date:** [October 4, 2022, 1:44pm UTC](https://gromacs.bioexcel.eu/t/mdrun-cgenff-charmm-error/4940/2 "2022-10-04T13:44:14Z")

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You’re using NetworkX 2.x with the script designed for NetworkX 1.11. Get the correct version and it should be fine. We do the version check in kind of a dumb way that sometimes fails, so as long as you are actually using suitable versions, you could disable the check if you want.

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**Author:** ![Rudhra](https://avatars.discourse-cdn.com/v4/letter/r/958977/32.png) [@Rudhra](https://gromacs.bioexcel.eu/u/Rudhra)\
**Post date:** [October 5, 2022, 9:27am UTC](https://gromacs.bioexcel.eu/t/mdrun-cgenff-charmm-error/4940/3 "2022-10-05T09:27:55Z")

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Dear Sir,

First of all, Thanks a million for your clarification and reply.

I have uninstalled networkx 2. 8 and installed networkX1.1. I got one new error, I did a google search, and found that I have to update older version 1.1 to new version 2. x to solve this error.

Could you tell me please how to disable the check? I don’t know how to do it.

I have attached an error screenshot for your perusal. If possible, suggest to me how to solve this error.

 ![network_error](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/a/a081ba5e591e216846b2d2822e5183b6563eb1d6.png)

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<div class="post-metadata">

**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\
**Post date:** [October 6, 2022, 5:35pm UTC](https://gromacs.bioexcel.eu/t/mdrun-cgenff-charmm-error/4940/4 "2022-10-06T17:35:01Z")

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If you are having issues with Python, its packages, or internal dependencies, Google is your friend. This isn’t a GROMACS issue. Simply entering that ImportError into Google gives you the answer in the first result:

> <https://stackoverflow.com/questions/66174862/import-error-cant-import-name-gcd-from-fractions>

We note which versions we have tested the code with. If you’re using a different version of anything, things may have changed that you will need to solve. We do not have the time or resources to test every combination of versions, unfortunately.