Description of the data and file structure

Atomic-level AMBER program (version 22) input and output files are provided for molecular dynamics (MD) setups and simulations of MIG6 (wildtype, G334R, S390N, and P377S variants) complexed EGFR and solvated in TIP3P water. In this repository, there are four mutations of pdb 4ZJV used for the corresponding work.

Files and variables

Download folder structure

Each tar.gz folder represents one of the four mutations.

1. wild-type or no_mut.tar.gz
2. G344R mutation or G344R_mut.tar.gz
3. S390N mutation or S390N_mut.tar.gz
4. P377S mutation or P377S_mut.tar.gz

Folder structure for each download xxx.tar.gz folder

Each xxx.tar.gz contains three folders:

1. 01_prep: prepared models for modeling using equilibration and production MD
2. 02_equi: input and output files for equilibrating models
3. 03_production: input and output files for production MD for only first seed (6 seeds total)

01_prep folder contents

Here, 01_prep contains the prepared models for the solvated (wet) and unsolvated (gas) in the form of .prmtop and .rst7 files.

1. 4zjv.gas.complex.prmtop: Topology for gas-phase complex
2. 4zjv.wet.complex.prmtop: Topology for solvated complex
3. 4zjv.gas.complex.rst7: Coordinates and velocities for gas-phase complex
4. 4zjv.wet.complex.rst7: Coordinates and velocities for solvated complex

02_equi folder contents

Here, 02_equi contains the input and outputs of the 9-step equilibration and minimization protocol. Please refer to the original work in Table 1. The folder will contain five file types:

• .info – Metadata or descriptive information

• .mdin – Input parameters for the MD simulation

• .mdout – Output logs from the MD run

• .rst7 – Restart files containing updated coordinates

• .trj – Trajectory files storing atomic positions during simulation

  Each file will have the protocol step number, min or equi tag, and the file type embbeded into the file names.

Naming convention:
Each file includes the step number, the type of step (min for minimization or equi for equilibration), and the file type.
For example:

• 01.min.trj → Trajectory file from step 1 (minimization)
• 03.equi.mdout → Output log from step 3 (equilibration)

For example:
01.min.trj means step one in the protocol (01), where it is the minimization (min) and its a trajectory file. (.trj)

03_production

Here, we have five files for the first seed of the production MD simulation.

• prod1.info – Descriptive info about this production run

• prod1.mdin – Input parameters for production MD
• prod1.mdout – Output log
• prod1.rst7 – Final restart file
• prod1.trj – Trajectory of the MD simulation

Software Used

The simulations and data were generated using tools from the AMBER22 software suite:

tleap – for system preparation

pmemd.mpi – for running the MD simulations in parallel

Both programs are included in the AMBER22 package.

Access information

Data was derived from the following sources:

• We used pdb system 4ZJV to prepare the wildtype and mutated models.