• 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.