GROMACS version: 2025.2
GROMACS modification: Yes/No
Hi, I would like to ask regarding my situation.
I have a graphene oxide .pdb file that has functional groups attached on both sides of the sheet (top and bottom), and also I have its .top file through AmberTools (tleap option).
In my case, I want to remove the functional groups at the top of my graphene sheet manually by deleting through PyMol or Schrodinger. However, I’m worried that it might affect my old topology file.
What should I do? I want to ask specific workflows regarding this, since the internet has limited resources for expertise.