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

Amber: How to set-up simple calculations (No Non-standard Residues ). Requirements. Amber Modules: xleap/tleap, sander Text Editor Visualization program (VMD or Chimera) Starting Coordinates (PDB). PDB Original. Topology File (prmtop ). Coordinate File (inpcrd). sander. Text Editor.

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Amber: How to set-up simple calculations (No 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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