acellera-modrna-params 0.1.4

OL3-consistent AMBER force-field parameters for modified RNA residues, generated with modXNA

acellera-modrna-params

OL3-consistent AMBER force-field parameters for modified RNA residues, generated with 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

pip install acellera-modrna-params

Usage

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).