Author: Eric Wang

Please email me at ericzwang@gmail.com if something isn't clear

Mutating a lipid means changing its chemical structure. We do this when our membrane contains a lipid which is not available by default in the CHARMM force field, but the structure is similar to an existing lipid. To mutate a lipid, you'll need to create your membrane with the pre-mutated lipids using CHARMM-GUI first.

Once that is done, modify the relevant .str file to include your mutated lipid. See the following path on DT2 for an example for mutating CER240 to CER6.
/lustre/ewang125/scripts/mutate/toppar_all36_lipid_sphingo.str

This mutation involved adding a few hydroxyls. When you add new atoms, you need to decide what the partial charges will be. You also may need to add new parameters for dihedrals or angles at the end of the .str file. CHARMM will give you an error if these are missing.

Mutate the lipids using mutate.inp An example is in the path
/lustre/ewang125/scripts/mutate/mutate.inp