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Amber: Simple Calculation Setup without Non-standard Residues

Learn how to set up basic calculations in Amber using xleap/tleap, sander, and a text editor. Follow a workflow for minimization and molecular dynamics utilizing starting coordinates in PDB format. Visualize results with VMD or Chimera.

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Amber: Simple Calculation Setup without Non-standard Residues

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  1. Amber: How to set-up simple calculations(No Non-standard Residues )

  2. Requirements • Amber Modules: xleap/tleap, sander • Text Editor • Visualization program (VMD or Chimera) • Starting Coordinates (PDB)

  3. PDB Original Topology File (prmtop) Coordinate File (inpcrd) sander Text Editor Xleap/tleap Control Data (mdin) PDB Modified Output Info (mdout) Final Coord (restrt) Simple Amber Setup Workflow(Minimization)

  4. Topology File (prmtop) Coordinate File (inpcrd) Control Data (mdin) sander Output Info (mdout) Final Coords(restrt) Sander Setup: Simple Minimization

  5. Output Info (mdout) Final Coords(restrt) MD Trajectory Coords (mdcrd) Sander Setup: Simple MD Topology File (prmtop) Coordinate File (inpcrd) Control Data (mdin) sander

  6. Sander Setup: Minimization with position restraints Topology File (prmtop) Coordinate File (inpcrd) Control Data (mdin) Reference Coords (refc) sander Output Info (mdout) Final Coords(restrt)

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