Hi everyone, I come from a biology background, so my knowledge of programming is limited. I'm doing the protein-ligand tutorial from the mdtutorials site for GROMACS. For the ligand topology, it says to use the CHARMM force field and the CGenFF server. Since CHARMM is an all-atom force field, the crystal structure of the ligand that was downloaded needs to include its hydrogens. As far as I remember, Avogadro was very buggy and couldn't be used for this. Version 2 also gave an output format of JSON and another one called Chemical Markup Language (CML). So, I used PyMOL to get a mol2 output because the CGenFF server accepts this format. The strange thing is that in the str output, the sections for atoms, bonds, and dihedrals are empty and have no data! I don’t know how to solve this.
Aside from this, I continued with the str file provided in the tutorial for checking. To convert the str file to a format readable by GROMACS (itp), I used cgenff_charmm2gmx (https://github.com/Lemkul-Lab/cgenff_charmm2gmx), but it kept giving weird errors! I checked the version of NetworkX and also numpy.
I'd appreciate any guidance.
