Re: [rDock-list-def] Tethering params

[Peter S. <pet...@gm...>]

Hi Tim,

are you docking compounds that generate important clashes when they are tethered? 

usually the MAX_TRANS and MAX_ROT parameters respond fairly well. We use for instance 0.1 & 0.1 for both often. 

Peter



> On 30 Apr 2020, at 16:41, Tim Dudgeon <tdu...@gm...> wrote:
> 
> 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
> 
> 
> 
> 
> 
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