[Dock-fans] Critical points docking

[Scott Brozell]

Hi,

On Fri, 14 Mar 2008, Dmitry Osolodkin wrote:

> can you help me with the docking with critical points? When I'm trying 
> to use critical points matching during docking, there is no difference 
> with results obtained without use of the critical points and ligand is 
> positioned far from my critical points in rather big binding site. Here 
> are notable diffs for input file and spheres file for both runs:
> 
> dock.in
> 8c8
> < receptor_site_file 
> /path/to/file/r1_selected_cp.sph
> ---
>  > receptor_site_file 
> path/to/file/r1_selected2.sph
> 10c10
> < critical_points                                              yes
> ---
>  > critical_points                                              no
> 
> $ diff r1_selected2.sph r1_selected_cp.sph
> 5,6c5,6
> <   725  -3.67366  -0.94941   6.66700   1.744 1170 0  0
> <  1155  -4.94955  -0.66937   6.87639   1.979 1599 0  0
> ---
>  >   725  -3.67366  -0.94941   6.66700   1.744 1170 1  0
>  >  1155  -4.94955  -0.66937   6.87639   1.979 1599 1  0
> 8,9c8,9
> <  1170  -3.66265  -1.15074   5.99243   1.969  725 0  0
> <  1173  -3.49529  -0.56780   7.36908   1.408  725 0  0
> ---
>  >  1170  -3.66265  -1.15074   5.99243   1.969  725 1  0
>  >  1173  -3.49529  -0.56780   7.36908   1.408  725 1  0
> 
> Is this mapping of critical points right? My guess is that I shouldn't 
> rebuild grids for critical points usage, is it right?

Yes the sphere file format is correct according to
http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#SphgenCriticalPoints
Yes I see no reason to rebuild grids.

Dock 6.2 contains code to read and check critical points.
It does not appear to be obviously wrong.
However, there are no tests or examples that use critical points.
I'm contacting other developers for the status of critical points.

In the mean time you could try the alternative mentioned in
http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#CriticalPoints
to determine whether your system is conducive to critical points.

Scott