First Molecule:
Submitting DNA (PDB)
Chain to be used - All
Segment ID for docking - A
Molecule type - DNA
Second Molecule:
Submitting ligand (PDB)
Chain to be used - All
Segment ID - B
Molecule type - protein/peptide/ligand
Distance Restraints:
Define randomly ambiguous interaction restraints from accessible residues - checked
Sampling parameters:
Number of structures for rigid body docking - 10000
Number of structures for semi-flexible refinement - 400
Number of structures for the explicit solvent refinement - 400
Clustering Parameters:
Clustering method - RMSD
RMSD cutoff - 2.0
Advanced Sampling:
initial temperature for second TAD cooling step with flexible side-chain at the inferface (i think that’s interface) - 500
initial temperature for third TAD cooling step with fully flexible interface - 300
number of MD steps for rigid body high temperature TAD - 0
number of MD steps during first rigid body cooling stage - 0
That’s all I have modified.
Please give some comment.