GROMACS version:2024.1
GROMACS modification: No
Force Field used: amber99sb.ff
I’m trying to modify the amber99sb.ff Foce Field for simulating the tripeptide containing D amino acids.
I adjusted parameter in this force field and wrote CDT instead of CT and change the aminoacid’s name; DALA instead of ALA.
Now I want to know how to edit my pdb file.
I guess change the Cα atoms type and change the resname for example DAL because this column can have three letters in pdb file.
Subseguently I need to re-editing the force field.
Do you think these steps are correct and functional?