ADL: Including water molecules in docking

Douglas Houston dhouston at
Fri Apr 3 07:18:13 PDT 2009

The waters already have hydrogens added using PDB2PQR (which I also  
use to add hydrogens to the receptor). This tries to predict positions  
based on optimal H-bonding network.

Quoting Florian Nachon <mailinglist at>:

> On 3 Apr 2009, at 15:37, Douglas Houston wrote:
>> Thanks Gavin,
>> If I use
>> / -U nphs_lps_nonstdres -r receptor.pdb
>> it seems to keep the waters while still doing everything else,
> You'll miss the protons, i.e. H-Bond donor atoms, but H-Bond acceptor
> is already a drastic improvement over no water molecule at all!
> Any software to predict the most likely position of these protons?
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Dr. Douglas R. Houston
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