GROMACS version: 2023.3
GROMACS modification: No?
Hey guys, I’ve had an issue for an extended period of time and still haven’t found the simplest way to solve it. So I used CHARMM-GUI to generate a membrane bilayer consisting of DPPC lipids, due to how they construct their lipids, the structure files contain the lipids seperated between head and tail groups - named PC and PA respectively - and are correctly numbered resid wise in the PDB file but are all numbered differently in the GRO file. I.e. since they occur as PA, PC, PA for one lipid, in the PDB file theyre numbered 1, 1, 1, but in the GRO file they’re numbered 1, 2, 3. On top of this, the PDB file doesn’t have the box size included while the GRO file does and using the editconf command to add the box doesn’t correctly add the box since the molecules are whole. I only require the lipids to have one resname - DPPC - and correctly numbered, I’ve tried a bunch of different things like making an index file and using gmx editconf but nothing seems to work bar manually editing the file. Since I’ll likely be using CHARMM-GUI alot to create bilayer I figured it would be best to seek some help. I’m sure I’m missing something super simple but I’m completely lost.
NOTE: I already manually edited the FF files so the molecule is correctly named so maybe thats causing some sort of issue?