I am trying to simulate Glyceryl monooleate (GMO) as the ligand in GROMACS, I am using the CHARMM36 port for GROMACS. CHARMM36 already has force field parameters for glycerol monostearate (GMS), which has 2 more hydrogen atoms than GMO only. My question is weather I can use the parameters of GMS for GMO by renaming the residues in the pdb file to match the residue name of GMS.
And if yes, then why is there a different set of parameters for the isomer of GMS (same chemical formula) ?
Thanks in advance.