ADL: Including water molecules in docking

Douglas Houston dhouston at
Fri Apr 3 06:37:08 PDT 2009

Thanks Gavin,

If I use

/ -U nphs_lps_nonstdres -r receptor.pdb

it seems to keep the waters while still doing everything else,



Quoting Gavin Seddon <home at>:

> Douglas Houston wrote:
>> Hi all,
>> I've noticed that in one of my structures there's a very   
>> stable-looking water molecule that might well allow for   
>> water-mediated hydrogen bonding when ligands bind. I also notice   
>> all water molecules get removed when converting the receptor pdb to  
>>  pdbq. Is there any way to get Autodock to use this water molecule,  
>>  for example perhaps by treating it as part of the binding site?
>> thanks for any input,
>> Doug
> Hi
> the python script
> uses a '-U' ARGUMENT that removes water, use scrpts, without -U and do
> other cleanup with alternate software; or prep molecule another way.
> This is a really interesting point.
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Dr. Douglas R. Houston
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