[Dock-fans] Chemical matching error

[Scott Brozell]

Hi,

On Thu, 30 Oct 2008, Donna wrote:

> I have applied flexible docking (anchor and grow) using DOCK6.2.
> The critical points seems to work fine and the ligands are docked in the area within the receptor.

Great !

> But when I apply both the critical points and chemical matching it doesn't work and I get this error message:
> 
> *** glibc detected *** dock6: free(): invalid next size (normal): 0x0000000017359440 ***
> 
> Does anyone know what this means and what to do?

It is possible that there are memory allocation/deallocation or other bugs;
in addition, input errors are possible.
You could start debugging; rebuild dock with -g and run dock under valgrind:
http://valgrind.org/

Or you could send me all the necessary inputs files to verfiy the bug
and start debugging.

Note that this is not the first report of problems with
critical points and/or chemical matching.
Those reports have not been forgotten.

> Below is short preview of my .sph file, which in total has 21 spheres (15 of which are labeled as critical and all 21 are chemically labeled;
> 
> color hydrophobic 1
> color donor 2
> color polar 3
> cluster     0   number of spheres in cluster    21
>     1  12.96100  22.23500  16.47200   2.000  0 1  1
>     2    3.81300  13.49700  13.81500   2.000  0 1  1
>     3    8.44800  11.29000  22.86200   2.000  0 1  2
>     4  14.39100  18.02200  23.03600   2.000  0 0  1
>     5    1.16500  11.52800  15.51800   2.000  0 1  3
>     6  14.14700  22.37900  17.21000   2.000  0 0  1
> 
> Does the chemical matching setup in my .sph file look correct?

It is consistent with
http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#SphgenChemicalMatching

Scott