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

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Presentation transcript:

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

Requirements 1.Amber Modules: xleap/tleap, sander 2.Text Editor 3.Visualization program (VMD or Chimera) 4.Starting Coordinates (PDB)

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

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

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

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