GROMACS version: 2023
GROMACS modification: No
Operating System: Ubuntu 22.10
This is an error I faced while following “Step Two: Prepare the Ligand Topology” of the Lemkul Labs’ GROMACS tutorial on Protein-Ligand Complex.http://www.mdtutorials.com/gmx/complex/02_topology.html
After using this command
python3 cgenff_charmm2gmx.py JZ4 jz4_fixed.mol2 jz4.str charmm36-mar2019.ff I get the following error:
My networkx version is 1.11, python version is 3.10.7 and I downloaded the corresponding python script i.e. cgenff_charmm2gmx_py3_nx1.py from the MacKerell Lab website http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs (I have renamed this script to the one given in the command above)
I have followed all the previous steps exactly as instructed in the tutorial, except that I used OpenBabel to convert the ligand (JZ4) pdb file to mol2 and add the hydrogens instead of doing the same with Avogadro. I have no idea what is causing this error and how to fix it.
Any help I receive will be much appreciated
PS: I would really like to know if there is any alternative method for generating the ligand’s topology using CHARMM that, hopefully, does not lead to errors like this.