# acellera-modrna-params

OL3-consistent AMBER force-field parameters for modified RNA residues,
generated with [modXNA](https://github.com/modxna/modxna).

This is a standalone GPL-3.0 package (see "Licensing"). It ships pre-generated
AMBER OFF libraries plus the shared `frcmod.modxna`, so downstream tools can
depend on it and load the files without needing modXNA or a generation step.

## Supported residues

Nine PDB residues, each in three chain-context forms (internal, 5'-terminal,
3'-terminal), following OL3's `G` / `G5` / `G3` convention. Unit names are the
PDB code with a `5`/`3` suffix for the terminal forms (e.g. `5MC`, `5MC5`,
`5MC3`).

| PDB | modXNA base | note |
|-----|-------------|------|
| 5MC | M5C | |
| PSU | PUU | modXNA `PSU` is a thiouracil; real pseudouridine is `PUU` |
| 5MU | M5U | |
| 2MG | M2G | modXNA `2MG` is N2,N2-dimethyl; mono-methyl is `M2G` |
| 1MG | M1G | |
| 2MA | M2A | |
| 1MA | M1A | |
| 4AC | A4C | |
| 6IA | I6A | |

## Install

```bash
pip install acellera-modrna-params
```

## Usage

```python
import modrna_params as mp

mp.RESIDUES                     # supported PDB codes
mp.frcmod_path()                # path to frcmod.modxna
mp.lib_path("5MC")              # internal form
mp.lib_path("5MC", "5prime")    # 5'-terminal form
mp.leaprc_lines()               # tleap loadamberparams/loadoff lines
```

In tleap:

```
source leaprc.RNA.OL3
loadamberparams <frcmod_path()>
loadoff <lib_path("5MC")>
x = sequence { G5 5MC G3 }
```

## Charge consistency with OL3

Internal residues are OL3-consistent: backbone and sugar atom charges match
OL3's standard nucleotides to ~0.001 e; only the glycosidic-junction atoms
(C1'/H1') shift, as expected for a base modification. Terminal caps carry
modXNA's own fitted charges and do not match OL3 per-atom. modXNA's terminal
split (5' = -0.320348, 3' = -0.679652) sums to -1.000, so a strand with the
modified residue internal, or modified at both termini, is integral; a strand
that mixes a modXNA-modified terminus with a standard OL3 terminus is
non-integral by ~0.012 e (it still builds; downstream neutralization handles
it).

## Licensing

The `.lib` files are derivative works of modXNA's GPL-3.0 fragment library and
`frcmod.modxna` is redistributed verbatim, so this package is GPL-3.0-only. See
`LICENSE` and `NOTICE`. Please cite modXNA (J. Chem. Theory Comput. 2024,
doi:10.1021/acs.jctc.4c01164).
