NodeNode / Manipulator

RMSD

Calculate the RMSD and maximum atomic displacement between a reference structure and a set of conformers. The set of atoms to superpose can be defined via an ASL expression. The following ASL expression has a special meaning:

  • all = all atoms in the reference and comparison structures
Note that the number of atoms used in the comparison has to be identical. This is usually not a problem with conformers of course but can be problematic when comparing different molecules and using the ASL expression 'all'.

Backend implementation

$SCHRODINGER/run rmsd.py
Input ports
  1. Molecules in Maestro format Type: Data
    Reference Molecule in Maestro format
  2. Molecules in Maestro format Type: Data
    Comparison Molecules in Maestro format
Output ports
  1. Molecules in Maestro format Type: Data
    Superposed Molecules in Maestro format
  2. Distance Matrix output Type: Data
    Matrix is calculated for all members of first input against all members of second input
  1. Conformational search analysis
    Molecular mechanics ConfGen Confromations +5
    Extract ligands from PDB structures and run ConfGen. Compare the conformations in terms of RMSD and intramolecular dist…
    schroedinger > Workflow_examples > Molecular Mechanics > Conformational search > MM Conformational search 1-4
  2. Conformational search analysis
    Molecular Mechanics ConfGen Conformations +5
    Extract ligands from PDB structures and run ConfGen. Compare the conformations in terms of RMSD and intramolecular dist…
    schroedinger > Workflow_examples > Molecular Mechanics > Conformational search > MM Conformational search 1-3
  3. Ligand alignment MD refinement
    Molecular Dynamics
    A Desmond molecular dynamics simulation is run on each ligand prealigned in the protein binding site. Then the represen…
    schroedinger > Workflow_examples > Molecular Dynamics > Ligand alignment MD refinement > Ligand alignment MD refinement 1-2
  4. Cocrystallized Ligand Redocking
    Real World Glide LigPrep +1
    Extract ligands from a set of PDB protein-ligand complexes. The complexes are then prepared and a Glide grid is generat…
    schroedinger > Workflow_examples > Real world > Cocrystallized ligand redocking > Cocrystallized ligand redocking 1-2
  5. Ligand alignment MD refinement
    Molecular Dynamics
    A Desmond molecular dynamics simulation is run on each ligand prealigned in the protein binding site. Then the represen…
    schroedinger > Workflow_examples > Molecular Dynamics > Ligand alignment MD refinement > Ligand alignment MD refinement 1
  6. Macrocyclization
    Prime Protein preparation
    Starting from a linear compound macrocyclizations are created, the conformations sampled and compared for a cocrystalli…
    schroedinger > Workflow_examples > Molecular Mechanics > Macrocyclization > Macrocyclization
  7. Cocrystallized Ligand Redocking
    Real World Glide LigPrep +1
    Extract ligands from a set of PDB protein-ligand complexes. The complexes are then prepared and a Glide grid is generat…
    schroedinger > Workflow_examples > Real world > Cocrystallized ligand redocking > Cocrystallized ligand redocking 1