Refinement of membrane dimeric protein with bound ligand

[Le-Phung-Hien]

Hi team,

I am trying to refine a Modeller-generated structure of a membrane dimeric protein with bound ligand. Is it going to be possible with PREFMD2?

Just want to ask since I see some hashed codes in prefmd2.py:

# arg.add_argument('--membrane', dest='is_membrane_protein',
# action='store_true')
# arg.add_argument('--ligand', dest='has_ligand', action='store_true')
# arg.add_argument('--oligomer', dest='is_oligomer', action='store_true')

which is exactly what my protein is.

Thanks!

[feiglab]

We are not supporting refinement of membrane proteins or structures with ligands in this version of our code as it involves additional complexities that require manual attention (ligand parameters, membrane type/width).

We recommend using other tools such as CHARMM-GUI to set up simulations of membrane-embedded systems with or without ligands and and run those simulations following our published refinement protocols instead of using the tool provided here.