GROMACS version:5.1.4
GROMACS modification: Yes/No
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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?
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.
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.
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:
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.