ADL: Hydrated Docking Problem

Stefano Forli forli at scripps.edu
Wed Aug 19 10:24:14 PDT 2020


Hi Manuel,

likely, what's happening is that non-optimal poses might be too close to the grid box edges so there are not enough points around the waters to allow proper scoring.

Nevertheless, I thought that bug was fixed, but I'm not sure if we updated the version that can be downloaded (could you tell me where you got the hydrated docking files and when you donwloaded them?).

Try running the attached version and see if it still triggers the error. After downloading it you have to remove the ".txt" extension (silly mail server limitations).

Let me know if it works.

Best,

S

On 8/19/20 9:36 AM, mllanos at biol.unlp.edu.ar wrote:
> Hi all,
> I'm having some problems trying to use the hydrated docking protocol
> It works fine until the dry.py step, where the program gives me this error when I try to run the full mode (-F) with DLG and W.map files as input:
> 
> Traceback (most recent call last):
>   File "./scripts/dry.py", line 1192, in <module>
>   harvest, affinity = getpoints(grid, coord(w), distance = 1.0) # angstroms
>   File "./scripts/dry.py", line 737, in getpoints
>   harvesting.append( data[z,y,x] )
> IndexError: index (53) out of range (0<=index<53) in dimension 1
> 
> If I run it with option -E (extract only LE pose, no LCLE) it works, but the generated PDBQT file can not converted back to PDB (I've tried with pdbqt_to_pdb.py script and Babel)
> 
> I'm using python interpreter from MGLtools
> 
> Thanks in advance
> best regards
> Manuel A. Llanos (http://www.linkedin.com/in/manuel-augusto-llanos/?locale=en_US) - Ph.D. Student
> Laboratory of Bioactive Research and Development (http://lideb.biol.unlp.edu.ar/) - LIDeB
> Faculty of Exact Sciences - National University of La Plata - Argentina.
> ________________________________________________
> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
> 

-- 

  Stefano Forli, PhD

  Assistant Professor
  Dept. of Integrative Structural
  and Computational Biology, MB-112A
  Scripps Research
  10550  North Torrey Pines Road
  La Jolla,  CA 92037-1000,  USA.

     tel: +1 (858)784-2055
     email: forli at scripps.edu
     http://www.scripps.edu/faculty/forli/
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