192
S. Sakkiah et al.
10.4.3 NAMD
NAMD is written in Charm++ [57]. It was developed by the Theoretical and Computational Biophysics Group (TCB) and Parallel Programming Laboratory (PPL) at
the University of Illinois at Urbana-Champaign.
The 3D structure of protein atomic coordinates from PDB, protein structure file
(psf), force field parameter file, and configuration files are prerequisites to running a
NAMD simulation. The initial protein 3D structure downloaded from PDB does not
contain hydrogen atoms because X-ray crystallography cannot resolve the hydrogen atoms. Hence, the command psfgen generates the pdb file with hydrogen atom
coordinates. The generated pdb file is subject to energy minimization to ensure reasonable atomic coordinates. The minimized protein coordination file is immersed in
a water box to adopt a cellular environment for the target protein. The protein can be
solvated in two ways for energy minimization and equilibration: (i) vacuum, without
periodic boundary conditions, or (ii) water box, with periodic boundary conditions.
The important features of NAMD are given below:
(1) Compatibility with the CHARMM force field to stimulate the systems. This
force field was used by other programs such as CHARMM and X-PLOR, hence
it is easy to migrate from one program to another as well as to analysis the
trajectory files.
(2) Efficiently utilization of the Particle Mesh Ewald algorithm—full electrostatic
interactions to reduce the electrostatic complexity.
(3) Leverages the Verlet integration method—multiple time steps are applied to
compute local interactions at each time step and to reduce the computational
cost for long-range interaction calculations.
(4) Variety of simulation options.
(5) Easy to modify and extend a given run.
(6) Interactive simulations.
10.4.4 Desmond
Desmond was developed by D. E. Shaw Research group using numerical methods
[58] and novel parallel algorithm [59] to run high-speed MD simulations for biological systems. It is integrated with the Maestro modeling environment (Schrodinger,
Inc), a commercial software package compatible with VMD and analysis tools.
Proteins directly downloaded from PDB are not suitable for dynamics analysis
because they lack hydrogen atoms and contain poorly defined bond orders and formal
charges. Hence, protein preparation is the initial and a very important step in MD
simulations. The basic steps to run MD simulations using Desmond from Maestro
are given below:
1. Import the protein 3D structure file either from PDB or from a homology modeling method into Maestro.
S. Sakkiah et al.
10.4.3 NAMD
NAMD is written in Charm++ [57]. It was developed by the Theoretical and Computational Biophysics Group (TCB) and Parallel Programming Laboratory (PPL) at
the University of Illinois at Urbana-Champaign.
The 3D structure of protein atomic coordinates from PDB, protein structure file
(psf), force field parameter file, and configuration files are prerequisites to running a
NAMD simulation. The initial protein 3D structure downloaded from PDB does not
contain hydrogen atoms because X-ray crystallography cannot resolve the hydrogen atoms. Hence, the command psfgen generates the pdb file with hydrogen atom
coordinates. The generated pdb file is subject to energy minimization to ensure reasonable atomic coordinates. The minimized protein coordination file is immersed in
a water box to adopt a cellular environment for the target protein. The protein can be
solvated in two ways for energy minimization and equilibration: (i) vacuum, without
periodic boundary conditions, or (ii) water box, with periodic boundary conditions.
The important features of NAMD are given below:
(1) Compatibility with the CHARMM force field to stimulate the systems. This
force field was used by other programs such as CHARMM and X-PLOR, hence
it is easy to migrate from one program to another as well as to analysis the
trajectory files.
(2) Efficiently utilization of the Particle Mesh Ewald algorithm—full electrostatic
interactions to reduce the electrostatic complexity.
(3) Leverages the Verlet integration method—multiple time steps are applied to
compute local interactions at each time step and to reduce the computational
cost for long-range interaction calculations.
(4) Variety of simulation options.
(5) Easy to modify and extend a given run.
(6) Interactive simulations.
10.4.4 Desmond
Desmond was developed by D. E. Shaw Research group using numerical methods
[58] and novel parallel algorithm [59] to run high-speed MD simulations for biological systems. It is integrated with the Maestro modeling environment (Schrodinger,
Inc), a commercial software package compatible with VMD and analysis tools.
Proteins directly downloaded from PDB are not suitable for dynamics analysis
because they lack hydrogen atoms and contain poorly defined bond orders and formal
charges. Hence, protein preparation is the initial and a very important step in MD
simulations. The basic steps to run MD simulations using Desmond from Maestro
are given below:
1. Import the protein 3D structure file either from PDB or from a homology modeling method into Maestro.