[Dock-fans] segmentation fault - Dock3.5 Score in Dock6.2

[John J. Irwin]

Hi Barbara

I think we generally only cut the protein if the number of
atoms/residues will overflow some fixed format field.  We tend to not do
this unless we must, and then we retain a wide radius - maybe 20 A
around the binding site, so any truncation effects are vanishingly small.

John


Collignon, Barbara C. wrote:
> Hi everybody,
>
> I wonder whether one has to cut the protein before using the DOCK3.5 score with the DOCK6.2 version ? 
> I mean, should I select only the residues around the active site?
>
> In fact. With the DOCK3.5 version, some people used the FILT program to reduce the target before docking. 
>
> However, according to the DOCK6.2 tutorial, we don't have to select a small part of the protein only.
> But for the DOCK3.5 score maybe we should... 
>
> Any advices ?
>
> Barbara 
>
>