[Dock-fans] ligand prepare

Scott Brozell sbrozell at scripps.edu
Tue Mar 6 09:38:19 PST 2007


On Sat, 24 Feb 2007, Qiang Zhong wrote:

>      I am a beginner of Dock,I have a ligand ,it is a part of protein, this part
> is  only 20 amino residues,On prepare stage, I use whole protein as a ligand ,then
> When  generating spheres, I execute:sphere_selector rec.sph lig_charged.mol2
> 10.0,the result selected_spheres.pdb is not I wanted,I think there must be some
> wrong when I use whole protein as a ligand, Could somebody tell me how to do?
>   I need whole protein and receptor as a complex to MD simulation, So docked
> complex need include whole protein and receptor.

The information is insufficient:
Why is the resulting selected_spheres.pdb not what you wanted ?
What do you suspect is wrong ?
Also more detail on 20 residue ligand vs whole protein might be useful.


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