[Dock-fans] Anchor size and clashes elimination

[Grzegorz Popowicz]

Hi all!
1. The default size of an anchor in DOCK is 40 atoms this generates quite  big 
fragments as for beginning of docking (at least 480Da). I have tried smaller 
anchors (8 atoms) with good results. Are there any rules governing selection 
of anchor size?
2. Dock run with use_clash_overlap=no generates solutions with terrible 
clashes (of course), however the predictions of known ligands binding are 
very good in my case. With use_clash_overlap=yes and clash_overlap=0.5 (BTW. 
What does percent of overlap mean?) there are no clushes but known ligands 
are badly docked and scored much much worse than without clashes filter. Is 
there any resonable explanation to this fact?

Gregor