GROMACS version:2023.1
GROMACS modification: Yes/No
Here post your question :
I want to run MD simulation on protein and LPS (a molecular located on the outer membrane of E.coli). When I use CGenff to convert the lps pdb into charmm36 format, I found CGenff can directly convert it into gromacs format and give many output files including new format .pdb file, lipidA.top file and other .itp files. So what files should i use for later simulation? I treid to add the .itp files in the lipid.top file into the protein.top file, but got error when I want to add ions. The files i added:
