Hi guys,
I am trying do clustering analysis with the Analyze Ligand Protocol. In the help topic, I learned there would we a "RMSD" floder in the outputs if I set RMSD=true and reference=All poses. I did set these. Below is my parameters:
But I cannot find the RMSD folder...the only thing I got was just a matrix of RMSD in the SD file as molecule properties. I am using the WIN version of DS 2.1... Anyone can tell me why I meet this problem?! Thanks in advance!!


Input Ligands ../Input/B12_1N4A-(1).sd
Input Receptor ../Input/B12_1N4A.msv
Hydrogen Bonds False
Hydrogen Bonds Scope Molecule
Hydrogen Bonds Label HBOND Count
Contacts False
Contacts Type All
Contacts Threshold
Contacts Scope Molecule
Contacts Label Contacts
RMSD True
RMSD Reference All Poses
RMSD Atom Group Heavy Atom
RMSD Label SmartRMSD to pose
ROC Curve False
ROC Curve Scores DOCK_SCORE
ROC Curve Group Using -PMF
ROC Curve Control Property
ROC Curve Control Value 1
ROC Curve Total Records 0
ROC Curve Total Positives 0
Parallel Processing False
Parallel Processing Batch Size 25
Parallel Processing Server localhost
Parallel Processing Server Processes 2
Parallel Processing Preserve Order TrueRMSD=true and reference=All poses