[Dock-fans] out_scored.mol2 file

Terry Lang terry at cgl.ucsf.edu
Wed Aug 31 11:43:18 PDT 2005

Dear Oshik,

          The molecules in the out_scored file are not ranked.  The file 
contains the best scoring pose for each ligand in the same order as the 
input library.  The file out_ranked should contain the ranked ligands if 
you set the "rank_ligands = yes" and the out_scored file should be 
empty. If you want the ligands written to the out_scored file as well 
(in the same order as the input library), you need to set the 
"scored_mol_output_override = yes"   If you send me your input file, I 
can look to see what files you should be getting and what each should 


oshik segev wrote:

> Hello dock-fans!
> I'm having problems with the output files I am getting. I'm running 
> DOCK5 on a subset from ZINC database and I allways get an output file 
> with many molecules in the out_scored file. Are the molecules in this 
> file ranked? How can I rank them, by the energy score or by the RMSD? 
> (In my input file the parameter out_ranked is YES and I get an empty 
> file).
> Thank you
> Oshik Segev
>Dock-fans mailing list
>Dock-fans at docking.org

P. Therese Lang
Kuntz and James Labs
UCSF--Chemistry and Chemical Biology
Phone: (415)476-3986


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