[Dock-fans] problem about the ranked result of DOCK6.2

[Scott Brozell]

Hi,

On Sun, 29 Mar 2009, CAI Qixu wrote:

> I have a serious problem. I screen a subset of small molecules in ZINC
> (about 170000 molecules), and I set the parameter "rank_ligands" to be "yes"
> and "max_ranked_ligands" to be "500"
> (1) Does it mean that in the process of docking, there is no output (because
> I find the ligand_outfile_prefix_ranked.mol2 is 0kb, and nothing is in the
> file after I have calculate 1000 molecules) ? And mol2 file and after all
> calculation finished, the final ranked mol2 file will generate, which have
> 500 ligands?

Yes, ligand_outfile_prefix_ranked.mol2 will be empty until all ligands
have been processed, and yes it will ultimately contain 500 ligands.

> (2) When the DOCK is docking, I split the mol2 file of the ZINC subset to
> two mol2 files, which contain 100000 molecules and 70000 molecules. And I
> overwrite the mol2(170000) with the mol2 file (100000) when the mol2(170000)
> is docking! I want to know whether  the docking process will stop at 170000
> molecules or 100000 molecules?

Hmm, Im not sure i understand your question.
Apparently, you used the same ligand_outfile_prefix for all 3 runs ?
If so then there will be problems.

Scott