GROMACS version: 2024.4
GROMACS modification: No
I am following the famous Justin Lemkul tutorials, I want to combine umbrella sampling with protein ligand complex. First I am having difficulties with the ligand force field parameters.
The tutorial provides a solution that doesn’t work for me. There is this repo:
All of these require a specific version of networkx that I fail to install, and the others I can don’t work.
On the CGenFF website there is an option to download the results in GROMACS format. I am assuming that this is probably an easier option, I just don’t know how to include the data.
https://www.dropbox.com/scl/fi/dvw98s1r0k1m12zjzqqdv/jz4_fix_gromacs.zip?rlkey=s6dkj3c5e5j2vm48k4vqa0exw&dl=0
(Link to the download compressed file)
They provide a folder charmm36.ff that contains 2 new files (maybe more?) “jz4.rtp” and “jz4_ffbonded.itp” (this last one contains only one line of values). There’s also 2 other files: “jz4_fix_gmx.pdb” and “jz4_fix_gmx.top”.
From the .pdb I’ve managed to get the .gro with:
gmx editconf -f jz4_fix_gmx.pdb -o jz4.gro
I know this is good, because it lines up with the information on the tutorials page.
There’s 2 more things that are missing however, the .itp and the .prm files. I know that the .itp is the topology and I have a .top file, but that`s not working if I just include it like that (the ligand won’t show up after I add the box, also it gives me a warning of “WARNING: Bad box in file complex.gro”) and the other 2 files from the charmm36.ff folder must be the parameter files, but again, just including them doesn’t work.
There is probably a better, maybe even easier way of doing this.