Hi all,
I am studying a protein (sandercyanin) and its ligand (biliverdin).
I wish to titrate some residues in the protein and together I wish to titrate the ligand. The ligand is biliverdin, a molecule with two carboxylic acids.
How does one go about setting up the parm file for non-standard ligands in AMBER? I am reading chapter 26.5 in the manual, but it doesn't describe how to approach poly-protic acids. Also, how should I approach the force field that will be used? Is there a specific force field for titrating organic molecules in igb=2 or can I just use gaff?
Thanks,
Lefteris
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Dec 19 2023 - 16:00:03 PST
