In the 1K1D PDB structure, there is a lysine-carboxylic acid ligand (KCX-150) connected to LEU-149 and ALA-151 by its N and C atoms, respectively. To calculate the parameters of separated hetero groups, I optimize them using the Gaussian package and then calculate them using the AMBER antechamber module.
What is the best way to calculate the parameters of this connected ligand?
Hi,
KCX-150 is lysine-like residue, right?
It is non-standard residue, and for amber, you can follow this tutorial:
https://ambermd.org/tutorials/basic/tutorial5/index.php
Simply, optimize the geometry first, then calculate the partial charges and create a topology file. Your approach is reasonable.
Moreover, In this case, it is linked to protein, I suggest calculating the partial charge of the side chain only, and not the backbone.
Kindly look into the supporting information.
https://pubmed.ncbi.nlm.nih.gov/34495791/