AMBER Examples

For Blacklight

Download blacklight example files here

Files include:

  • amber.job, PBS script
  • mdin, input file
  • inpcrd, input coordinates
  • prmtop, input file for molecular topology, force field, periodic box type and atom and residue names
  • logfile, output data
  • mdout, user readable state info and diagnostics (output)
  • mdinfo, latest md-format energy info (output)
  • restrt, final coordinates, velocity and box dimensions for a restart run
  • amber.out, standard output and error

For Salk

Download salk example files here

Files include:

  • amber10.job, PBS script
  • mdin, input file
  • inpcrd, input coordinates
  • prmtop, input file for molecular topology, force field, periodic box type and atom and residue names
  • logfile, output data
  • mdout, user readable state info and diagnostics (output)
  • mdinfo, latest md-format energy info (output)
  • restrt, final coordinates, velocity and box dimensions for a restart run
  • amber10.out, standard output and error
 

More on AMBER

Example jobs

Documentation

The AMBER Home Page (Scripps) which includes links to tutorials, and Amber documentation.

User Information

PSC Passwords

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PSC Policies

For technical questions:
Call the PSC hotline: 412-268-6350 / 800-221-1641 or mail to remarks@psc.edu.

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