[Dock-fans] About amber scoring

Kim Branson kim.branson at gmail.com
Mon Oct 9 19:58:57 PDT 2006


you can specify individual residues using nab.
the amber manual (chapter 7) has more detail on how to write nab  
queries.

the amber manual is freely accessible from the amber web site.

kim


On Oct 9, 2006, at 7:41 PM, xxffliu at 163.com wrote:

>  Dear dockers:
>  I'm interested in DOCK6's new function in amber scoring, because  
> it's claimed to support "induced fit" docking in some way. I just  
> wonder can I define a sphere of residues within some range of the  
> ligand as flexible region instead of the whole receptor in case to  
> reduce computation cost. It's seemed that the NAB expressions  
> mentioned in the mannul doesn't support this query. I would  
> appreciate your kindly reply.
> Good DOCKing!!
>
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