PINANG is a collection of tools for molecular dynamics.
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README.org

README.org

pinang

Description

This is a package consisting of several small handy tools for analyzing biomolecule structures (protein, RNA, DNA) or MD trajectories.

At the current stage, these tools are mainly used for analyzing CafeMol MD results.

Installation

Please change compiler confirgurations in src/Makefile, then run

make
make install

By default, all the tools will be moved to the bin/ directory.

Prerequisites

The Boost C++ Libraries are reqired.

Tools

CommandDescription
p_cafemol_ts_readSimplely read CafeMol .ts files.
p_dcd_angle_comCalculate angle between three COMs (center of masses).
p_dcd_base_pairing_percentageCalculate base pairing percentage for DNA.
p_dcd_contact_numberCalculate contact number between biomolecule chains.
p_dcd_distance_*Calculate distances between atoms/COM/specified groups.
p_dcd_dna_curvatureCalculate DNA curvature from trajectories.
p_dcd_interface_scanFind inter-chain interface in MD trajectories.
p_dcd_persistence_lengthCalculate DNA persistence length from MD trajectories.
p_pdb_PDI_stStatistics of protein-DNA interactions from PDB structures.
p_pdb_R_gCalculate radius of gyration \(R_g\) of molecules from PDB.
p_pdb_catRe-output PDB coordinates.
p_pdb_cg_topGenerate topology file from PDB file.
p_pdb_dna_curvatureCalculate DNA curvature and other structural information from PDB.
p_pdb_get_sequenceOutput sequence of molecules in PDB.

Dangerous Traps

PDB format

  • DNA residues should have name “DA”, “DT”, “DC”, or “DG”.
  • If the user want to include ions into CG models, change atom record name from “HETATM” to “ATOM”.