-
pdb
: the Protein Data Bank file. More information is available in the
PDB files section.
-
prepi
: an AMBER PREP internal coordinate file. This is one file which
allows non-standard residues to be added to the AMBER database for your
simulation. More specific information is available in
the AMBER documentation.
-
mol2
: the Tripos Mol2, printed in ASCII format, that was developed for
molecular visualization. It contains information about the atom (including
coordinates and charges), in addition to bonds and any relevant aspects
of the structure.
-
frcmod
: modified force field parameters. These are critically important for
non-standard residues. More specific information is available in
the AMBER documentation.
-
lib
: an OFF library file containing information about non-standard
residues. The generation of this file is preferred for larger co-enzymes,
instead of other treatments for non-standard residues. More specific
information is available in
the AMBER documentation.
-
mdin
: input files that control simulation conditions and settings for data
collection.
-
prmtop
: the molecular topology file. More specific information is available
in the AMBER documentation.
-
inpcrd
: coordinate files. These are preferred by parm and LEaP, but is
almost equal to an rst
.
-
rst
: restart files that contain information about the last frame’s energy
minimization or molecular dynamics information from sander or gibbs. They
get their name from being used to restart a simulation from them, instead of
starting from the beginning again.
-
mdcrd
: a trajectory file. These contain information on coordinates
throughout the course of the simulation.
-
nc
: a NetCDF file. While the manuals/guides I’ve written tend talk about
this as a file generated after cpptraj processing, it’s really just anything
written in NetCDF. Technically, then, everything generated with or after
AMBER16 using an mdin file without ntxo=1
(for ASCII rst files) and ioutfm=0
(for ASCII mdcrd files) should have the
nc
extension for both trajectory and restart information. That said, the
default to NetCDF was a recent change, and people using the former mdcrd
extension may not have changed their naming to the nc
extension.