[rDock-list-def] Tethering params

[Tim D. <tdu...@gm...>]

I'd like a clarification on the use of tethering parameters (the LIGAND 
section of the configuration file).

I started by using the default parameters that seem to be recommended:

SECTION LIGAND
     TRANS_MODE TETHERED
     ROT_MODE TETHERED
     DIHEDRAL_MODE FREE
     MAX_TRANS 1
     MAX_ROT 30
END_SECTION

The results show that the poses are tethered but the tethering is 
relatively weak. So I tightened up the params to this

SECTION LIGAND
     TRANS_MODE TETHERED
     ROT_MODE TETHERED
     DIHEDRAL_MODE FREE
     MAX_TRANS 0.2
     MAX_ROT 5
END_SECTION

But this had very minimal impact. The poses we still fairly weakly 
tethered. I would have expected the pose to be pretty well anchored to 
the position of the tethered atoms.

Finally I tried FIXING the positions using:

SECTION LIGAND
     TRANS_MODE FIXED
     ROT_MODE FIXED
     DIHEDRAL_MODE FREE
END_SECTION

Not sure if this is supported. I was hoping that it fixes the tethered 
atoms but allows the other ones to move. But what happened is that some 
of the tethered atom were pretty well fixed, but others moved widely.

Can someone explain?

Thanks
Tim