[Dock-fans] How to parameterize halide ion ligand

[Scott Brozell]

Hi,

On Wed, 17 Sep 2008, Francesco Pietra wrote:

> I am now ready to attempt docking of small molecules onto a large
> protein. Ready, except for what concerns halide ion ligands present in
> the protein.
> 
> The model (from Modeller) saved the spatial relationship of the
> made-punctiform halide ion. With DOCK, in procedure all movable, such
> restriction would be overridden.Any suggestion how to let DOCK know
> about the vdw radious of the halide ion?

DOCK has support for halide ions:
parameters/vdw_AMBER_parm99.defn

"in procedure all movable"
does this refer to Amber score with
amber_score_movable_region=everything ?
The scaffolding for ions was added in 6.2 and chloride has been
added in 6.3beta.  

Scott