ADL: Hydrated Docking Problem

mllanos at biol.unlp.edu.ar mllanos at biol.unlp.edu.ar
Thu Aug 20 16:59:20 PDT 2020


Hi Stefano,
Yass it's working now !

Thanks for your help

best,

manu

21 de agosto de 2020 0:50, "Stefano Forli" <forli at scripps.edu> escribió:

> 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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