Molecular Dynamics and FEP Setup

This repository contains scripts for setting up and running molecular dynamics (MD) simulations and free energy perturbation (FEP) calculations using GROMACS and related tools.

Prerequisites

Before using these scripts, ensure you have the following software installed:

• Python (3.7 or higher). Recommended to create a Conda environment:

  conda create -n py37 python=3.7
  conda activate py37

• PyModSim: Install via GitHub.
• PyMemDyn: Install via GitHub.
• LigParGen: Install via GitHub.
• GROMACS: Required for MD simulations.
• Schrödinger Maestro (or equivalent software) for protein and ligand preparation.

Workflow Overview

Step 1: Align Complex with PyModSim

Before proceeding with the provided scripts, the PyModSim tool must be used to align the protein-ligand complex with the membrane. This step ensures that the system is properly oriented for subsequent docking and molecular dynamics simulations.

Instructions for PyModSim Execution

1. Prepare Input Files:

   • Export the protein and ligand from Schrödinger Maestro (or other software) as separate PDB files.

2. Run PyModSim:

   pymodsim -n 3 -p unaligned_protein.pdb

   Replace unaligned_protein.pdb with the name of your protein file.

3. Output: PyModSim generates a properly aligned protein file in finalOutput/homology.pdb that can be used as input for the next steps.

Note: Ensure the complex is visually inspected after alignment to confirm correctness.

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Step 2: Ligand Modelling or Docking

This protocol was tested by using Schrödinger Maestro. After docking, export protein and ligands as separated pdb files.

Step 3: Prepare System for PyMemDyn

Use the setup_pym.py script to prepare ligand-receptor systems for PyMemDyn simulations.

Usage

python setup_pym.py [--noclean] [-C CLUSTER] [-p PROTEIN]
                    [-l LIGAND] [-w WATERS] [-i IONS]
                    [-r RESTRAINT] [--fep]

Argument	Description
--noclean	Retain intermediate files.
-C CLUSTER	Specify the cluster for job submission (CSB, CESGA, TETRA).
-p PROTEIN	Protein PDB file (default: protein.pdb).
-l LIGAND	Ligand identifier in the PDB (default: LIG).
-w WATERS	Crystallized water identifiers (default: HOH).
-i IONS	Crystallized ion identifiers (default: NA).
-r RESTRAINT	Restraint type: bw (Ballesteros-Weinstein) or ca (C-alpha). Default: ca.
--fep	Prepare files for FEP calculations (adds --full_relax false to PyMemDyn execution).

The script:

1. Creates a folder for each ligand.
2. Generates the ligand-receptor complex.
3. Runs LigParGen for ligand parameterization.
4. Prepares SLURM scripts (pymemdyn.sh for PyMemDyn execution and submit_pym.sh for batch submission).

Input Structure:

my_project/
├── protein.pdb
├── ligand1.pdb
├── ligand2.pdb

Output Structure:

my_project/
├── 1.input_files/
│   ├── protein.pdb
│   ├── ligand1.pdb
│   ├── ligand2.pdb
├── ligand1/
│   ├── complex.pdb
│   ├── LIG.gro
│   ├── LIG.itp
│   └── pymemdyn.sh
├── ligand2/
├── submit_pym.sh

Submit PyMemDyn jobs:

sh submit_pym.sh

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Step 3: Setup MD Simulations

After PyMemDyn equilibration, use the setup_md.py script to prepare MD simulation files.

Usage

python setup_md.py [-t TIME] [-rt RUNTIME] [-C CLUSTER] [-n NUM_REPLICAS]

Argument	Description
-t TIME	Simulation time in nanoseconds (default: 25).
-rt RUNTIME	Runtime limit in hours (default: 36).
-C CLUSTER	Cluster for job submission (CSB, CESGA, TETRA).
-n NUM_REPLICAS	Number of replicas for MD simulations (default: 3).

The script:

1. Copies required files to a 3.md/ directory.
2. Prepares SLURM scripts for MD simulations (run_md.sh for each replica and submit_md.sh for batch submission).
3. Modifies prod.mdp to set the simulation time and random seed.

Input Structure:

my_project/
├── 1.input_files/
│   ├── protein.pdb
│   ├── ligand1.pdb
│   ├── ligand2.pdb
├── ligand1/
│   ├── complex.pdb
│   ├── LIG.gro
│   ├── LIG.itp
│   └── pymemdyn.sh
├── ligand2/
├── submit_pym.sh

Output Structure:

my_project/
├── 1.input_files/
│   ├── protein.pdb
│   ├── ligand1.pdb
│   ├── ligand2.pdb
├── 2.pymemdyn/
│   ├── ligand1/
│   ├── ligand2/
├── 3.md/
│   ├── lig1_1 <- Replica 1 ligand 1
│   │   ├── LIG.itp         
│   │   ├── ffoplsaa_mod.itp
│   │   ├── index.ndx  
│   │   ├── posre.itp      
│   │   ├── posre_NA.itp  
│   │   ├── run_md.sh <- SLURM execution for MD
│   │   ├── topol.tpr
│   │   ├── LIG_backup.itp  
│   │   ├── ffoplsaabon_mod.itp  
│   │   ├── ions.itp   
│   │   ├── posre_HOH.itp
│   │   ├── prod.mdp <- Modified with setup_md.py
│   │   ├── spc.itp
│   │   ├── confout.gro
│   │   ├── ffoplsaanb_mod.itp
│   │   ├── popc.itp
│   │   ├── posre_LIG.itp
│   │   ├── protein.itp
│   │   ├── topol.top
│   ├── lig1_2 <- Replica 2 ligand 1
│   ├── lig1_n <- Replica n ligand 1
│   └── submit_md.sh <- Calls run_md.sh inside each directory

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License

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Acknowledgments

• PyMemDyn
• PyModSim
• LigParGen

For issues or contributions, contact ruben.prieto@usc.es.