# Frequently asked questions (FAQ)

## Input files for applying SMIRNOFF parameters

SMIRNOFF force fields use direct chemical perception meaning that, unlike many molecular mechanics (MM) force fields, they apply parameters based on substructure searches acting directly on molecules. This creates unique opportunities and allows them to encode a great deal of chemistry quite simply, but it also means that the starting point for parameter assignment must be well-defined chemically, giving not just the elements and connectivity for all of the atoms of all of the components of your system, but also providing the formal charges and bond orders.

Specifically, to apply SMIRNOFF to a system, you must either:

1. Provide Open Force Field Toolkit `Molecule` objects corresponding to the components of your system, or

2. Provide an OpenMM `Topology` which includes bond orders and thus can be converted to molecules corresponding to the components of your system

Without this information, our direct chemical perception cannot be applied to your molecule, as it requires the chemical identity of the molecules in your system – that is, bond order and formal charge as well as atoms and connectivity. Unless you provide the full chemical identity in this sense, we must attempt to guess or infer the chemical identity of your molecules, which is a recipe for trouble. Different molecules can have the same chemical graph but differ in bond order and formal charge, or different resonance structures may be treated rather differently by some force fields (e.g. `c1cc(ccc1c2cc[nH+]cc2)[O-]` vs `C1=CC(C=CC1=C2C=CNC=C2)=O`, where the central bond is rotatable in one resonance structure but not in the other) even though they have identical formal charge and connectivity (chemical graph). A force field which uses the chemical identity of molecules to assign parameters needs to know the exact chemical identity of the molecule you are intending to parameterize.

## Can I use an AMBER (or GROMACS) topology/coordinate file as a starting point for applying a SMIRNOFF force field?

In a word, “no”.

Parameter files used by typical molecular dynamics simulation packages do not currently encode enough information to identify the molecules chemically present, or at least not without drawing inferences. For example, one could take a structure file and infer bond orders based on bond lengths, or attempt to infer bond orders from force constants in a parameter file. Such inference work is outside the scope of SMIRNOFF.

If you have such an inference problem, we recommend that you use pre-existing cheminformatics tools available elsewhere (such as via the OpenEye toolkits, such as the `OEPerceiveBondOrders` functionality offered there) to solve this problem and identify your molecules before beginning your work with SMIRNOFF.

## What about starting from a PDB file?

PDB files do not in general provide the chemical identity of small molecules contained therein, and thus do not provide suitable starting points for applying SMIROFF to small molecules. This is especially problematic for PDB files from X-ray crystallography which typically do not include proteins, making the problem even worse. For our purposes here, however, we assume you begin with the coordinates of all atoms present and the full topology of your system.

Given a PDB file of a hypothetical biomolecular system of interest containing a small molecule, there are several routes available to you for treating the small molecule present:

- Use a cheminformatics toolkit (see above) to infer bond orders

- Identify your ligand from a database; e.g. if it is in the Protein Data Bank (PDB), it will be present in the Ligand Expo meaning that it has a database entry and code you can use to look up its putative chemical identity

- Identify your ligand by name or SMILES string (or similar) from the literature or your collaborators

## What do you recommend as a starting point?

For application of SMIRNOFF force fields, we recommend that you begin your work with formats which provide the chemical identity of your small molecule (including formal charge and bond order). This means we recommend one of the following or equivalent:

- A `.mol2` file or files for the molecules comprising your system, with correct bond orders and formal charges. (Note: Do NOT generate this from a simulation package or tool which does not have access to bond order information; you may end up with a `.mol2` file, but the bond orders will be incorrect)

- Isomeric SMILES strings for the components of your system

- InCHI strings for the components of your system

- Chemical Identity Registry numbers for the components of your system

- IUPAC names for the components of your system

Essentially, anything which provides the full identity of what you want to simulate (including stereochemistry) should work, though it may require more or less work to get it into an acceptable format.