ADL: Hydrated Docking Problem

Stefano Forli forli at scripps.edu
Thu Aug 20 15:46:59 PDT 2020


Hi Manuel,

that is an unexpected error. Could you try to change the line 1092 from
   > lelc = get_lelc(structures[0])
to
   > lelc = get_lelc(input_file)

and see if it works?

About the binding affinity, the idea behind the normalized values generated with this method is exactly what you mentioned, allowing to account for the contribution of displaced waters to the overall binding energy, and (hopefully) enrich results.

In the tests we did for the paper, it was working fairly well, but my recommendation is to not to mix results from standard docking and hydrated dockings.

Hope this helps,

S


On 8/20/20 1:07 PM, mllanos at biol.unlp.edu.ar wrote:
> Hi Stefano,
> Thanks for your prompt response
> I had version v.1.1 and this version v.1.3 seems to work in full mode
> However, analyzing LE pose from hydrated simulations doesn't seems to improve RMSD values so I'm trying to analyze LELC
> When I try to run with option "-C" (extract the lowest energy-largest cluster result, strip all waters (if present) and save the file (DLG input only)) I get the following error:
> 
> Traceback (most recent call last):
>    File "../../../scripts/dry.py", line 1092, in <module>
>      lelc = get_lelc(structures[0])
> IndexError: list index out of range
> 
> If I use option "-c", it finds the LELC pose and write the pdbqt but it's not dry
> 
> Regarding binding affinity, the normalized value written to the dry file can be used for scoring validation (like ROC curves) ??
> 
> Best
> 
> Manu
> 
> 19 de agosto de 2020 19:34, "Stefano Forli" <forli at scripps.edu> escribió:
> 
>> Manuel,
>>
>> it seems the mailserver did't let the file through. please try downloading the file from here:
>> https://www.dropbox.com/s/75hht7wua121dzv/dry.py?dl=0
>>
>> Let me know if you have problems accessing it.
>>
>> S
>>
>> On 8/19/20 10:24 AM, Stefano Forli wrote:
>>
>>> 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.
>>>> ________________________________________________
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>>>
>>> ________________________________________________
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>>
>> --
>>
>> 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
>>
>> ________________________________________________
>> --- ADL: AutoDock List --- http://autodock.scripps.edu/mailing_list ---
> 
> 
> ________________________________________________
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> 

-- 

  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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