Understanding where to begin in Amber is primarily a problem of managing the flow of information in this package. You first need to understand what information is needed by the energy programs (gibbs, sander, roar and nmode). You need to know where it comes from, and how it gets into the form that the energy programs need. This section is meant to orient the new user, and is not a substitute for the individual program documentation.
Information that all the energy programs need:
This information is provided to the energy programs in three files: One contains the coordinates; the second contains the topology and parameters, and is called the "topology file"; the command or "input" file is the third file. Additional files may needed for special options specified in the command file.
Cartesian coordinates usually come from Xray crystallography, NMR spectroscopy, or model-building. They should be in Brookhaven Protein Databank (PDB) format. The program LEaP provides a platform for carrying out many of these modeling tasks, but users may wish to consider other programs as well.
Topology comes from the database, which is found in the $AMBERHOME/dat directory, and is described in Chapter 3. It contains topology for the standard amino acids as well as N and C-terminal charged amino acids, DNA, and RNA. The database contains default internal coordinates for these monomer units, but coordinate information is usually obtained from PDB files. Topology information for other molecules (not found in the standard database) is kept in user-generated "residue files".
The basic force field parameters are also found in the $AMBERHOME/dat directory; the database section of the manual contains some detailed descriptions of various force field options. This file may be used "as is" for proteins and nucleic acids, or users may prepare their own files that contain modifications to the "standard" force fields.
linethick=1.5 PDB: circle radius 0.4 "pdb" right arrow 0.75 from PDB.e LEAP: box "LEaP" move down from PDB.s RESTRAINTS: circle radius 0.4 "NMR" "info" down arrow 0.75 from LEAP.s "prmtop" "prmcrd" MD: box height 0.75 "sander," "gibbs," "roar" move down right 0.6 from MD.s ANAL: box "ptraj" move down from MD.s PTRAJ: box "mm-pbsa" move down left 0.6 from MD.s CARNAL: box "anal," "carnal" arrow from MD.se to ANAL.n arrow from MD.sw to CARNAL.n arrow from MD.s to PTRAJ.n right move 0.75 from LEAP.e NMODE: box "nmode" arrow from LEAP.e to NMODE.w "prmtop" above "prmcrd" below arrow down from NMODE.s box "nmanal," "lmanal" arrow from RESTRAINTS.e to MD.w