README for the AA_PTM_Hassan24.v2 force field (8/26/25).

Authors:
George Wanes
Paul Whitford (p.whitford@northeastern.edu)


Included Files:
AA_PTM_Hassan24.v1.b
AA_PTM_Hassan24.v1.bif
AA_PTM_Hassan24.v1.extras
AA_PTM_Hassan24.v1.nb
AA_PTM_Hassan24.v1.sif
AA_PTM_Hassan24.v1.map (for use with smog_adjustPDB)


General description:
This template is based on the SBM_AA-amber-bonds template that is 
available on the smog-server template repo. It has been extended
to include a range of RNA residues that have posttranscriptional 
modifications.

For a detailed description of AA_PTM_Hassan24.v1, see:
Singh, Itoh, Del'Olio, Hassan, Naschberger, Flygaard, Nobe, Izumikawa, Aibara, Andrell, Whitford, Barrientos, Taoka, and Amunts.
Mitoribosome structure with cofactors and modifications reveals mechanism of ligand binding and interactions with L1 stalk
Nature Communications, 15, 4272, 2024. 
DOI: 10.1038/s41467-024-48163-x

In relation to AA_PTM_Hassan24.v1, this version identical except that two ligands (NAD, SAH) have been introduced, as described in:
Zgadzay, Mirabello, Wanes, Panek, Chauhan, Nystedt, Zikova, Whitford, Gahura, and Amunts.
Mettl15-Mettl17 modulates the transition from early to late pre-mitoribosome
Structure, 2025.
DOI: 10.1016/j.str.2025.08.002


Model Resolution:
All non-H atoms are explicitly represented in RNA and proteins. Water molecules are not included.


Supported residues and atoms:
Standard protein and RNA residues, as well as some modified RNA and protein residues. See .map file for full list of supported residues.

* Modified nucleotides:
2MU
OMG
1MA
2MG
4OC
5MU
OMU
MA6
5MC
2MA
PSU
B8T

* Modified amino acids
AYA
SAC
THC
D1E

* Ligands 
SAH
NAD


Aspects built upon earlier models:
The distributions of stabilizing energetic terms (i.e. dihedrals vs. contacts) were assigned consistent with Whitford et al, Proteins (2009) and Noel et al. PLOS Comp Bio (2016). 

The contact map is based on the Shadow Contact Map algorithm (Noel, et al. JCP 2012) with a 6A cutoff with 1A atom radius.

The minimum for each contact is positioned at 0.96 times the native distance.  This was first introduced in simulations of the ribosome (Nguyen and Whitford, Nature Comm, 2016) to avoid artificial expansion. That is, the SMOG model defines the potential energy minimum. If native distances are used, then the free-energy minimum is slightly expanded, due to entropic contributions. We have found that, generally, scaling by 0.96 ensures that the native distance is very close to the free-energy minimum (at T=0.5 reduced units).

The bond lengths and distances are assigned the values given in the AMBER FF03 force field (Duan, et al. JCC 2003), as employed in a previous AMBER-SMOG model (Whitford, et al. Viruses 2020. SMOG 2 Force Field Repo ID: SBM_AA-amber-bonds). Similarly, planar dihedrals are assigned cosine potentials with periodicity 2. 

The atom nbtype for added atoms was determined by examining the atom types defined 
in the Amber force field at
http://www.chem.cmu.edu/courses/09-560/docs/msi/ffbsim/B_AtomTypes.html#636660 
(These atom types appear in Weiner et. al. 1984 & Weiner et. al. 1986)
and checking the atom type that corresponds to the added atom based on the chemical 
environment (expected hybridization state based on bond order, being present in an 
aromatic structure or not, being bonded with another known atom type, etc).

After adding the atoms and determining their atom nbtypes, the extra bonds are added 
under the bonds section, and any extra improper dihedral angles that are needed to 
conserve chirality or maintain planarity are added to the impropers section. For most 
of these modified residues, the added atoms are added to the nucleobases and thus no 
additional improper angles are needed.


Version Information:
These templates are intended for use with SMOG 2, version 2.3 and later.

