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ParmFit Tutorials

Get to know ParmFit’s parameterization workflow by solving a few simple examples.

Before you start: install AmberTools and Gaussian 16

Every case needs AmberTools. Every NCAA and MetalAA case, and Refinement Cases 2 and 3, also need Gaussian 16 for their RESP charges — the Refinement cases also for their QM reference; only Refinement Case 1 runs without it. MAPLE looks for Gaussian only when a run reaches its first Gaussian job, so a missing g16 stops the run partway through.

The Systems

Refinement Ball-and-stick render of o-iodophenol: a benzene ring bearing a large iodine ball and a hydroxyl group

o-Iodophenol

A phenol with an iodine beside its hydroxyl.

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NCAA Ball-and-stick render of the capped HF1 residue running diagonally across the frame: backbone caps and the large histidine-FAD sidechain

FAD in 6JQH

A histidine residue carrying a covalent FAD cofactor.

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MetalAA Ball-and-stick render of the 4ZF6 iron site: heme and cysteine donors with slate balls on the five donor atoms around the red iron sphere

HEME in 4ZF6

A cysteine-ligated heme iron site.

Start the tutorial →

Before You Start

  • Requirements. Software and input needs are summarized in the ParmFit hub’s Requirements section.
  • Model. Every run in these tutorials uses the same checkpoint — UMA-S-1.1, selected with #model=uma(size=uma-s-1p1) (the Refinement launchers add task=omol).
  • Hardware. Every excerpt and timing in these tutorials comes from runs on an RTX 3060 Laptop GPU and an 8-core AMD CPU — sufficient for every run shown here. Every Gaussian job used the defaults qm_nproc=8 and qm_mem=24 (GB); set lower values in the sidecar config on a smaller machine (see General Settings).