ADL: Including water molecules in docking

Gavin Seddon home at gavsed.net
Sat Apr 4 04:24:08 PDT 2009


Douglas Houston wrote:
> 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 nachon.net>:
>
>>
>> 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?
>> ________________________________________________
>> --- ADL: AutoDock List --- http://autodock.scripps.edu/mailing_list ---
>
>
>
>
> _____________________________________________
> Dr. Douglas R. Houston
> Room 3.23
> Institute of Structural and Molecular Biology
> Michael Swann Building
> King's Buildings
> University of Edinburgh
> Edinburgh, EH9 3JR, UK
> Tel. 0131 650 7358
>
again Whatif calculates its own H net


More information about the autodock mailing list