10 Applications of Molecular Dynamics Simulations …
191
tiple classical molecular force fields for nucleic acids, small molecules, and amino
acids and contains parameters for solvents, lipids, and carbohydrates. AMBER is
not a single source MD simulation program but instead provides a set of programs
that can run together. The atomic coordinates of the simulation system, the molecular topology file, force fields, and a script with all commands are prerequisites to
running.
LEaP, tleap or xleap, is command line programs which generate or modify the
parameter files for a new system or the existing systems. These programs convert most
of the chemical structure file types (such as mol2 and pdb) to AMBER parameter file
types (.lib, .prepi, parm.dat, and .frcmod). The energy minimization and dynamics
simulation parameter files contain key information required to run the simulation.
These commands also generate topology (.prmtop, .parm7, or .top) and coordination
(.inpcrd and .crd) files based on the parameter files.
The pdb4AMBER command converts pdb files from different sources like X-ray,
nuclear magnetic resonance, and homology modeling to a format suitable to LEaP.
The parmed command is used to validate and extract parameter information from
the parameter–topology file for the simulation system. This command also makes
minor modifications to parameter–topology file.
The AntechAMBER command uses the general AMBER force field (GAFF) to
generate and modify the parameter files for small molecules and amino acids.
The program sander is used to execute the energy minimization, equilibration,
and production runs. Sander interactively relaxes the system by iteratively moving
the atoms until a suitable low average gradient is reached. The system configuration
files are automatically generated during the production run by integrating Newtonian
equations of motion. The final production run generates a configurational space and
allows the structure to cross over smaller potential energy barriers than the energy
minimization. During dynamics simulations, the configuration of the system is saved
at the regular time interval for later analysis. Thermodynamic integration is used to
calculate system free energy. Sander module is used to study protein conformational
search, protein structure modeling, and structural refinement of proteins.
The program pmemd (Particle Mesh Ewald Molecular Dynamics) is the updated
version of sander with increased speed via parallel scaling during the production run.
The required pmemd input and output files are very similar to sander.
The program mdgx is a dynamics engine written in C and sorts the atoms to simplify the information flow during force calculation. It adopts select features from
pmemd and sander. The most common use of mdgx is redesign of dynamics algorithms or models to support parameters for new models.
The program mdout_analyzer.py is a simple Python script which summarizes the
information from pmemd or sander output files. The program Cpptraj, written in
C++, analyzes trajectory files such as coordinate extractions, RMSD, RMSF, bond
and angle calculations, and hydrogen bond analysis. The Python program pytraj has
flexibility to analyze data from trajectory files.
191
tiple classical molecular force fields for nucleic acids, small molecules, and amino
acids and contains parameters for solvents, lipids, and carbohydrates. AMBER is
not a single source MD simulation program but instead provides a set of programs
that can run together. The atomic coordinates of the simulation system, the molecular topology file, force fields, and a script with all commands are prerequisites to
running.
LEaP, tleap or xleap, is command line programs which generate or modify the
parameter files for a new system or the existing systems. These programs convert most
of the chemical structure file types (such as mol2 and pdb) to AMBER parameter file
types (.lib, .prepi, parm.dat, and .frcmod). The energy minimization and dynamics
simulation parameter files contain key information required to run the simulation.
These commands also generate topology (.prmtop, .parm7, or .top) and coordination
(.inpcrd and .crd) files based on the parameter files.
The pdb4AMBER command converts pdb files from different sources like X-ray,
nuclear magnetic resonance, and homology modeling to a format suitable to LEaP.
The parmed command is used to validate and extract parameter information from
the parameter–topology file for the simulation system. This command also makes
minor modifications to parameter–topology file.
The AntechAMBER command uses the general AMBER force field (GAFF) to
generate and modify the parameter files for small molecules and amino acids.
The program sander is used to execute the energy minimization, equilibration,
and production runs. Sander interactively relaxes the system by iteratively moving
the atoms until a suitable low average gradient is reached. The system configuration
files are automatically generated during the production run by integrating Newtonian
equations of motion. The final production run generates a configurational space and
allows the structure to cross over smaller potential energy barriers than the energy
minimization. During dynamics simulations, the configuration of the system is saved
at the regular time interval for later analysis. Thermodynamic integration is used to
calculate system free energy. Sander module is used to study protein conformational
search, protein structure modeling, and structural refinement of proteins.
The program pmemd (Particle Mesh Ewald Molecular Dynamics) is the updated
version of sander with increased speed via parallel scaling during the production run.
The required pmemd input and output files are very similar to sander.
The program mdgx is a dynamics engine written in C and sorts the atoms to simplify the information flow during force calculation. It adopts select features from
pmemd and sander. The most common use of mdgx is redesign of dynamics algorithms or models to support parameters for new models.
The program mdout_analyzer.py is a simple Python script which summarizes the
information from pmemd or sander output files. The program Cpptraj, written in
C++, analyzes trajectory files such as coordinate extractions, RMSD, RMSF, bond
and angle calculations, and hydrogen bond analysis. The Python program pytraj has
flexibility to analyze data from trajectory files.