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

Molecular Dynamics Simulation Files Description<br>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.<br>1. Initial Structure Files<br>- WT-2-new.pdb : Initial structure of the wild-type protein–DNA dimer complex. -prop.pdb : Alternative structural file for the same system. <br>2. Topology Files<br>- 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. <br>3. Position-Restraint Files<br>- 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<br>These files contain position restraints for the protein, DNA, and ion chains, which are applied during energy minimization and equilibration steps. <br> 4. Parameter Files (MDP)<br>- 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. <br>5. Index File<br>- index.ndx : Custom index file defining atom groups (e.g., protein, DNA, solvent, ions) used in analysis or restraint definitions. <br>6. Output Files<br>- 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.<br><br>- 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.