MD Simulation Pipeline

Protein Structure Input

Upload PDB File

Drag and drop your PDB file here or click to browse

Fetch from PDB

PDB ID:

Structure Preparation for AMBER

Prepare the protein structure for AMBER force field generation by cleaning and modifying the PDB file.

Remove Components

Remove water molecules

Remove all water molecules (HOH, WAT, TIP3, etc.) from the structure

Remove ions

Remove all ions (Na+, Cl-, K+, Mg2+, etc.) from the structure

Remove hydrogen atoms

Remove all hydrogen atoms from the protein structure

Add Capping Groups and Select Protein Chains

Add NME group (C-terminal)

Add N-methyl amide (NME) group to C-terminal residues

Add ACE group (N-terminal)

Add acetyl (ACE) group to N-terminal residues

Preserve Chains for FF Generation:

Select one or more protein chains to include in preparation

Ligand Handling

Preserve ligands

Keep ligands in the structure and append them at the end

Create separate ligand file

Extract ligands to a separate PDB file for individual processing

Select Ligands to Preserve

Tick ligands to include. Unselected ligands will be ignored.

Simulation Parameters

System Setup

Box Type:

Distance (Å):

Ligand Force Field

Ligand Force Field:

Force Field & Water Model

Protein Force Field:

Water Model:

Add Ions:

Temperature & Pressure

Temperature (K):

Pressure (atm):

Thermostat:

Integration Parameters

Time Step (ps):

Cutoff Distance (Ang):

Electrostatic:

Simulation Steps Configuration

Restrained Minimization

Steps:

Force Constant (kJ/mol/Å²):

Minimization

Steps:

Algorithm:

NPT Heating

Steps:

Target Temperature (K):

NPT Equilibration

Steps:

Temperature (K):

Pressure (atm):

Production Run(NPT)

Steps:

Temperature (K):

Pressure (atm):

MD Simulation Pipeline

Protein Structure Input

Upload PDB File

Fetch from PDB

Protein Preview

Structure Preparation for AMBER

Remove Components

Add Capping Groups and Select Protein Chains

Ligand Handling

Preparation Status

Prepared Structure Preview

Simulation Parameters

System Setup

Ligand Force Field

Force Field & Water Model

Temperature & Pressure

Integration Parameters

Simulation Steps Configuration

Restrained Minimization

Minimization

NPT Heating

NPT Equilibration

Production Run(NPT)

Generate Simulation Files

Generated Files

Download Files

Simulation Summary