ADL: Including water molecules in docking

Florian Nachon mailinglist at nachon.net
Fri Apr 3 07:03:03 PDT 2009


On 3 Apr 2009, at 15:37, Douglas Houston wrote:

> Thanks Gavin,
>
> If I use
>
> /prepare_receptor4.py -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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