[Dock-fans] How to get a score for xtallographic pose using DOCK

Terry Lang terry at cgl.ucsf.edu
Thu May 11 10:29:45 PDT 2006


Dear Zhenxuan,

          You can get a score from the original crystallographic pose 
before docking has been done. For the fastet preparation time, you need 
to convert your pdb files into mol2 files with charges and then perform 
continuous scoring.  For the dock input file, you need to set:

orient_ligand                          no
flexible_ligand                       no
bump_filter                            no
score_molecules                   yes
contact_score_primary          no
contact_score_secondary   no
grid_score_primary               no
grid_score_secondary         no
continuous_score_primary   yes
continuous_score_secondary yes

and then answer the other appropriate questions.  As a warning, though, 
using continuous scoring during docking is EXTREMELY slow.  Most people 
use grids-based scoring, which is orders of magnitude faster but adds a 
bit of error to the calculation.  If you want the interaction energy for 
a grid-based docking calculation, you will need to generate a grid and 
the set grid_score_primary and grid_score_secondary to "yes."

Sincerely,
Terry


Zhenxuan wrote:

> Hi all,
>  
> I am a new DOCK user. May I know is there anyway to get a score for 
> the original xtallographic pose even before docking has been done?
>  
> Thank you
>  
> Cheers,
> Zhenxuan
>
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-- 
P. Therese Lang
Kuntz and James Labs
UCSF--Chemistry and Chemical Biology
Phone: (415)476-3986

 





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