How niransha/amber_force_field_develeopment_scripts works
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 RMSD cluster summary · any_rna_double_helix_seq.sh Sequence builders · modify_RCSB_pdbs_and_change_resnames.sh PDB modification · slurm_scripts HPC job scripts
Components 18
Structure preparation
- Sequence builders
any_rna_double_helix_seq.sh - PDB modification
modify_RCSB_pdbs_and_change_resnames.sh - Residue parameters
create_newRESNAMEs.pl - Topology setup
xleap/xleap.new.in
Simulation
- MD initialization
create_init_md.pl - MD production
production_run.pl - HPC job scripts
slurm_scripts
Trajectory analysis
- Trajectory combining
cpptraj.combine_md_all.sh - RMSD analysis
cpptraj.rmsd.sh - Trajectory clustering
cluster.dbscan.cpptraj.hpc.sh - Torsion analysis
cpptraj.torsion_analysis.sh - Trajectory visualization
trajectory_analysis_scripts/rmsd_align_trajec_vmd.tcl - RMSD cluster summary
frame_vs_FirstAllRMSD_vs_minCluster_minRMSD.py
Energy fitting
- Fourier energy fit
LLSF.py
Other components
- Researcher
- QM–MM energy data
- RMSD input data
- Cluster summary output
Connections 6
- 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