AMBER is a popular Molecular Mechanics/Molecular dynamics package.
There are 69 different programs distributed under AMBER. Of them three are parallel.
For example, sander.LES, sander etc.
PMEMD: Particle Mesh Ewald Molecular Dynamics is an implementation of AMBER/Sander functions optimized for periodic PME and GB simulations.
Parallel AMBER programs have been compiled using LAM-MPI libraries (/opt/nasapps/build/LAM714/Lam-714/lib) The parallel versions of AMBER programs will have a ".MPI" suffix. For example, pmemd.MPI, sander.LES.MPI, sander.MPI
Please note that pmemd is available only in parallel mode.
To run any amber programs: Make sure /opt/nasaspps/bin is in your path, and type the executable program name. For example, xleap, tleap etc.
AmberTools consists of several independently developed packages that work with AMBER. Even though it is supposed to work closely with AMBER. It by itself can also function as a separate software package.
The main components of AmberTools are:
Nucleic Acid Builder, Leap, gleap, Antechamber, Ptraj
/opt/nasapps/stow/amber10/bin
if /opt/nasapps/bin is included in the User's path. They can access all the software packages of AmberTools.
For example, to use leap, type
leap
Nucleic Acid Builder (nab) is a high-level language and facilitates manipulations of macromolecules and fragments. nab uses C-like syntax for variables, expressions and control structures (if, for ..). In short it is a programming language. To use nab, one need to use intel compilers
For instance, to compile a nab program.
nab -o program_1 program_1.nab
Antechamber Suite is a set of tools to generate files for organic molecules.
location: /opt/nasapps/bin/antechamber
Program to READ/PRINT/PROCESS AMBER files and trajectories
/opt/nasapps/bin/rdparm /opt/nasapps/bin/ptraj