ADL: Including water molecules in docking

Gavin Seddon home at gavsed.net
Sat Apr 4 04:22:24 PDT 2009


Florian Nachon wrote:
>
> 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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>
Yes I help develop and use Whatif for this. It protonates, will add 
'possible' waters adds H bonds. In short it is a good protein research 
tool. Google 'whatif vriend'
gs


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