Mechanistic Insights into the Allosteric Regulation of P53 Y220C by Small-Molecule Stabilizers

Molecular Dynamics Simulation Files Description

This directory contains the input files and output results for GROMACS molecular dynamics (MD) simulations of protein–DNA complex and molecule-protein–DNA complex systems. Below is a detailed description of each file category.
As an example, the provided WT-2-new.pdb file represents the wild-type protein–DNA dimer complex.

1. Initial Structure Files

- WT-2-new.pdb : Initial structure of the wild-type protein–DNA dimer complex.
-prop.pdb : Alternative structural file for the same system.

2. Topology Files

- topol.top: Main topology file that links all components.
- topol_Protein_chain_A.itp / topol_Protein_chain_B.itp : Topology files for the two protein chains.
- topol_DNA_chain_C.itp / topol_DNA_chain_D.itp : Topology files for the two DNA chains.
- topol_Ion_chain_E.itp / topol_Ion_chain_F.itp : Topology files for ions.

3. Position-Restraint Files

- posre_Protein_chain_A.itp / posre_Protein_chain_B.itp
- posre_DNA_chain_C.itp / posre_DNA_chain_D.itp
- posre_Ion_chain_E.itp / posre_Ion_chain_F.itp

These files contain position restraints for the protein, DNA, and ion chains, which are applied during energy minimization and equilibration steps.

4. Parameter Files (MDP)

- em.mdp : Parameters for energy minimization.
-nvt.mdp : Parameters for NVT equilibration.
- npt.mdp : Parameters for NPT equilibration.
- md.mdp : Parameters for the production MD simulation.
- ions.mdp : Parameters for ion addition.

5. Index File

- index.ndx : Custom index file defining atom groups (e.g., protein, DNA, solvent, ions) used in analysis or restraint definitions.

6. Output Files

- md_01.log: The log file of the molecular dynamics simulation, containing details such as energy, temperature, pressure, and performance information. It is useful for checking whether the simulation has run correctly.

- md_01.gro: The final coordinate file of the system after the molecular dynamics run. This file can be used for further analysis or as the input for restarting/continuing the simulation.