# niransha/amber_force_field_develeopment_scripts architecture

> Architecture diagram of the GitHub repository niransha/amber_force_field_develeopment_scripts, generated by GitDiagram from its file tree, README and a sample of source files (last updated 2026-09-25). It is an AI-made overview: check details against the source.

- Interactive diagram: https://gitdiagram.com/niransha/amber_force_field_develeopment_scripts
- Repository: https://github.com/niransha/amber_force_field_develeopment_scripts

## Overview

This repository is a collection of scripts for nucleic-acid structure preparation, molecular-dynamics simulation, and trajectory/energy analysis. The apparent user workflow runs from sequence or PDB preparation through parameterization and simulation to structural analysis. The README is empty and sampled source covers only two analysis scripts, so the broader branches are represented from filenames and their wiring is left unspecified. The sampled RMSD script explicitly reads and writes named data files; LLSF.py reads a hard-coded energy-data path and fits Fourier coefficients.

Main entry points: [`frame_vs_FirstAllRMSD_vs_minCluster_minRMSD.py`](https://github.com/niransha/amber_force_field_develeopment_scripts/blob/main/frame_vs_FirstAllRMSD_vs_minCluster_minRMSD.py) (RMSD cluster summary), [`any_rna_double_helix_seq.sh`](https://github.com/niransha/amber_force_field_develeopment_scripts/blob/main/any_rna_double_helix_seq.sh) (Sequence builders), [`modify_RCSB_pdbs_and_change_resnames.sh`](https://github.com/niransha/amber_force_field_develeopment_scripts/blob/main/modify_RCSB_pdbs_and_change_resnames.sh) (PDB modification), [`slurm_scripts`](https://github.com/niransha/amber_force_field_develeopment_scripts/tree/main/slurm_scripts) (HPC job scripts)

## Diagram (Mermaid)

```mermaid
flowchart TD

subgraph group_prep["Structure preparation"]
  node_sequence["Sequence builders"]
  node_pdb["PDB modification"]
  node_resnames["Residue parameters"]
  node_topology["Topology setup<br/>[xleap.new.in]"]
end

subgraph group_sim["Simulation"]
  node_mdinit["MD initialization<br/>[create_init_md.pl]"]
  node_production["MD production<br/>[production_run.pl]"]
  node_scheduler["HPC job scripts"]
end

subgraph group_analysis["Trajectory analysis"]
  node_combine["Trajectory combining"]
  node_rmsd["RMSD analysis<br/>[cpptraj.rmsd.sh]"]
  node_cluster["Trajectory clustering"]
  node_torsion["Torsion analysis"]
  node_viz["Trajectory visualization"]
  node_rmsd_summary["RMSD cluster summary"]
end

subgraph group_energy["Energy fitting"]
  node_energyfit["Fourier energy fit<br/>[LLSF.py]"]
end

node_user(("Researcher"))
node_energydata["QM–MM energy data"]
node_rmsddata["RMSD input data"]
node_summarydata["Cluster summary output"]

node_user -->|"provides sequence"| node_sequence
node_user -->|"provides structure"| node_pdb
node_user -->|"submits jobs"| node_scheduler
node_energydata -->|"reads"| node_energyfit
node_rmsddata -->|"reads"| node_rmsd_summary
node_rmsd_summary -->|"writes"| node_summarydata

click node_sequence "https://github.com/niransha/amber_force_field_develeopment_scripts/blob/main/any_rna_double_helix_seq.sh"
click node_pdb "https://github.com/niransha/amber_force_field_develeopment_scripts/blob/main/modify_RCSB_pdbs_and_change_resnames.sh"
click node_resnames "https://github.com/niransha/amber_force_field_develeopment_scripts/blob/main/create_newRESNAMEs.pl"
click node_topology "https://github.com/niransha/amber_force_field_develeopment_scripts/blob/main/xleap/xleap.new.in"
click node_mdinit "https://github.com/niransha/amber_force_field_develeopment_scripts/blob/main/create_init_md.pl"
click node_production "https://github.com/niransha/amber_force_field_develeopment_scripts/blob/main/production_run.pl"
click node_scheduler "https://github.com/niransha/amber_force_field_develeopment_scripts/tree/main/slurm_scripts"
click node_combine "https://github.com/niransha/amber_force_field_develeopment_scripts/blob/main/cpptraj.combine_md_all.sh"
click node_rmsd "https://github.com/niransha/amber_force_field_develeopment_scripts/blob/main/cpptraj.rmsd.sh"
click node_cluster "https://github.com/niransha/amber_force_field_develeopment_scripts/blob/main/cluster.dbscan.cpptraj.hpc.sh"
click node_torsion "https://github.com/niransha/amber_force_field_develeopment_scripts/blob/main/cpptraj.torsion_analysis.sh"
click node_viz "https://github.com/niransha/amber_force_field_develeopment_scripts/blob/main/trajectory_analysis_scripts/rmsd_align_trajec_vmd.tcl"
click node_rmsd_summary "https://github.com/niransha/amber_force_field_develeopment_scripts/blob/main/frame_vs_FirstAllRMSD_vs_minCluster_minRMSD.py"
click node_energyfit "https://github.com/niransha/amber_force_field_develeopment_scripts/blob/main/LLSF.py"

classDef toneNeutral fill:#f8fafc,stroke:#334155,stroke-width:1.5px,color:#0f172a
classDef toneBlue fill:#dbeafe,stroke:#2563eb,stroke-width:1.5px,color:#172554
classDef toneAmber fill:#fef3c7,stroke:#d97706,stroke-width:1.5px,color:#78350f
classDef toneMint fill:#dcfce7,stroke:#16a34a,stroke-width:1.5px,color:#14532d
classDef toneRose fill:#ffe4e6,stroke:#e11d48,stroke-width:1.5px,color:#881337
classDef toneIndigo fill:#e0e7ff,stroke:#4f46e5,stroke-width:1.5px,color:#312e81
classDef toneTeal fill:#ccfbf1,stroke:#0f766e,stroke-width:1.5px,color:#134e4a
class node_sequence,node_pdb,node_resnames,node_topology toneBlue
class node_mdinit,node_production,node_scheduler toneAmber
class node_combine,node_rmsd,node_cluster,node_torsion,node_viz,node_rmsd_summary toneMint
class node_energyfit toneRose
class node_user,node_energydata,node_rmsddata,node_summarydata toneIndigo
```

## Components

### Structure preparation

- [Sequence builders](https://github.com/niransha/amber_force_field_develeopment_scripts/blob/main/any_rna_double_helix_seq.sh): `any_rna_double_helix_seq.sh`
- [PDB modification](https://github.com/niransha/amber_force_field_develeopment_scripts/blob/main/modify_RCSB_pdbs_and_change_resnames.sh): `modify_RCSB_pdbs_and_change_resnames.sh`
- [Residue parameters](https://github.com/niransha/amber_force_field_develeopment_scripts/blob/main/create_newRESNAMEs.pl): `create_newRESNAMEs.pl`
- [Topology setup](https://github.com/niransha/amber_force_field_develeopment_scripts/blob/main/xleap/xleap.new.in): `xleap/xleap.new.in`

### Simulation

- [MD initialization](https://github.com/niransha/amber_force_field_develeopment_scripts/blob/main/create_init_md.pl): `create_init_md.pl`
- [MD production](https://github.com/niransha/amber_force_field_develeopment_scripts/blob/main/production_run.pl): `production_run.pl`
- [HPC job scripts](https://github.com/niransha/amber_force_field_develeopment_scripts/tree/main/slurm_scripts): `slurm_scripts`

### Trajectory analysis

- [Trajectory combining](https://github.com/niransha/amber_force_field_develeopment_scripts/blob/main/cpptraj.combine_md_all.sh): `cpptraj.combine_md_all.sh`
- [RMSD analysis](https://github.com/niransha/amber_force_field_develeopment_scripts/blob/main/cpptraj.rmsd.sh): `cpptraj.rmsd.sh`
- [Trajectory clustering](https://github.com/niransha/amber_force_field_develeopment_scripts/blob/main/cluster.dbscan.cpptraj.hpc.sh): `cluster.dbscan.cpptraj.hpc.sh`
- [Torsion analysis](https://github.com/niransha/amber_force_field_develeopment_scripts/blob/main/cpptraj.torsion_analysis.sh): `cpptraj.torsion_analysis.sh`
- [Trajectory visualization](https://github.com/niransha/amber_force_field_develeopment_scripts/blob/main/trajectory_analysis_scripts/rmsd_align_trajec_vmd.tcl): `trajectory_analysis_scripts/rmsd_align_trajec_vmd.tcl`
- [RMSD cluster summary](https://github.com/niransha/amber_force_field_develeopment_scripts/blob/main/frame_vs_FirstAllRMSD_vs_minCluster_minRMSD.py): `frame_vs_FirstAllRMSD_vs_minCluster_minRMSD.py`

### Energy fitting

- [Fourier energy fit](https://github.com/niransha/amber_force_field_develeopment_scripts/blob/main/LLSF.py): `LLSF.py`

### Other components

- **Researcher**
- **QM–MM energy data**
- **RMSD input data**
- **Cluster summary output**

## Connections

- Researcher → Sequence builders: provides sequence
- Researcher → PDB modification: provides structure
- Researcher → HPC job scripts: submits jobs
- QM–MM energy data → Fourier energy fit: reads
- RMSD input data → RMSD cluster summary: reads
- RMSD cluster summary → Cluster summary output: writes