Implementing pairwise 12-6-4 LJ potential using tLEaP

Figure 2.1: A phosphate-water-ion system with solvent C₄ (indicated black) and modified C₄ (indicated green) terms

Learning Outcomes

Learn to apply pairwise C₄ terms using tLEaP

Overview

This is a extended tutorial to run an MD simulation using PMEMD.cuda in AMBER24 where metal->water, ligand->water, and metal<->ligand C₄ interactions are applied using the novel addC4Pairwise and addC4Type keyword. Please note that this tutorial does not require ParmEd, but will not work for AMBER version prior to (including) AMBER22AmberTools23.

Introduction

In AMBER24's PRMTOP file, the two tLEaP commands (addC4Pairwise and addC4Type) will generate three entries: LENNARD_JONES_CCOEF which was previously generated by ParmEd only, but now can be generated by addC4Type in tLEaP. LENNARD_JONES_DCOEF and LENNARD_JONES_DVALUE that save information for the atom-specific pairwise C₄ interaction.

Methods:

Step-by-step explanation:

```
tleap -s -f leap.in
```
This requires MOL.frcmod, MOL.mol2, MOL.pdb.

sed "s/o   o   o   o   /o-  o-  o-  o-  /g" resultPO4-nocount5_addc4.prmtop > temp && mv temp resultPO4-nocount5_addc4.prmtop

This is to rename the atom type manually to fulfill criteria #1 (atom type names must have "+" or "-" in them to enable C₄).

pmemd.cuda -O -i md_min1.in -o md_min1.out -p resultPO4-nocount5_addc4.prmtop
    -c resultPO4-nocount5.inpcrd -r md_min1.rst -x md_min1.netcdf -inf md_min1.mdinfo
    -ref resultPO4-nocount5.inpcrd

The first step of minimization should give a VDW energy of about 5888 kcal/mol.

By Zhen Li