ADL: Including water molecules in docking
dhouston at staffmail.ed.ac.uk
Fri Apr 3 06:37:08 PDT 2009
If I use
/prepare_receptor4.py -U nphs_lps_nonstdres -r receptor.pdb
it seems to keep the waters while still doing everything else,
Quoting Gavin Seddon <home at gavsed.net>:
> 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,
> 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.
> --- ADL: AutoDock List --- http://autodock.scripps.edu/mailing_list ---
Dr. Douglas R. Houston
Institute of Structural and Molecular Biology
Michael Swann Building
University of Edinburgh
Edinburgh, EH9 3JR, UK
Tel. 0131 650 7358
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.
More information about the autodock