Scripts for ff15ipq ligand parameter derivation

This directory provides an example of how to derive ff15ipq compatible parameters for a monastrol small molecule using slurm based HPC resources.

Branches

• Use the main branch if you're deriving parameters for a new molecule
• For an example of what that output files look like, see the monastrol branch

Dependencies:

• AmberTools
• Amber (pmemd)
• ORCA

The workflow is as follows:

• generate a pdb file of your small molecule or ligand
  • this can be done using something like Avogadro
  • in Avogadro, the molecule can also be energy minimized (recommended)
• derive a set of implicitly polarized (ipq) atomic partial charges for your molecule
  • see the /charges directory
  • note that this directory is currently set up to handle neutral molecules, if your molecule is charged, some adjustments are needed, as detailed in the charges directory
• optimize the initial set of bonded force field parameters that were roughly estimated in the charge derivation step
  • this is done in vacuo and uses the finalized vacuum phase atomic charges
  • see the /bonded directory
• you will now have an finalized library file containing the atomic charges and a frcmod file containing the bonded parameters for your molecule of interest
  • load these files into tleap along with the ff15ipq force field and you're good to go!

See the following publications for more information about the ff15ipq protein force field:

• KT Debiec, DS Cerutti, LR Baker, AM Gronenborn, DA Case, and LT Chong. “Further along the road less traveled: AMBER ff15ipq, an original protein force field built on a self-consistent physical model.” J. Chem. Theory Comput. 2016, 12, 3926. https://doi.org/10.1021/acs.jctc.6b00567
• AT Bogetti, HE Piston, JMG Leung, CC Cabalteja, DT Yang, AJ DeGrave, KT Debiec, DS Cerutti, DA Case, WS Horne, and LT Chong. “A twist in the road less traveled: The AMBER ff15ipq-m force field for protein mimetics.” J. Chem. Phys. 2020, 153(6), 064101. https://doi.org/10.1063/5.0019054
• DT Yang, AM Gronenborn, LT Chong, “Integrating Fluorinated, Aromatic Amino Acids into the Framework of the AMBER ff15ipq Force Field.” J. Phys. Chem. A, 2022, in press; https://doi.org/10.1021/acs.jpca.2c00255

A more detailed tutorial of the ipq parameter derivation process is available:

• IPQ Charges: https://ambermd.org/tutorials/advanced/tutorial28/index.php
• IPQ Bonded Parameters: https://ambermd.org/tutorials/advanced/tutorial32/index.php