ADL: Flexible Docking

Ruth Huey rhuey at scripps.edu
Thu Dec 4 10:25:45 PST 2014


Hi Monu,
________________________________________
From: autodock-bounces at scripps.edu [autodock-bounces at scripps.edu] On Behalf Of bharat lal [monu46010 at yahoo.com]
Sent: Monday, December 01, 2014 8:25 PM
To: autodock at scripps.edu
Subject: Re: Flexible Docking

Hi,
I have a query regarding flexible docking. I have selected a few residues as flexible for my receptor and when I analyze the docking results, the analyzer also shows the hydrogen bonds those flexible residues make apart from the hbonds made by the ligand. I want to know is it normal or not, because I think the energy for a particular pose will be calculated using the hydrogen bonds made those flexible residues as well. I don't know where am I going wrong, is the selection of flexible residues or something else. Moreover, when I checked the ligand file in the autodock panel, it also contained atoms from the receptor which I made flexible apart from the ligand atoms. Can anybody please clarify what could be the problem and how can it be rectified?
I have another query regarding grid generation using pick an atom option. 
How does that work? I mean whenever I select that option and check click any of the atom the grid doesnot move to that location.

>>This IS quite obscure and not well-documented:
By default, to move the box to a picked atom requires a "Pick-Shift" event.  That is, you must hold down the Shift key while you click on the atom.  When you chose the 'Center'-> 'Pick an atom ' option,  the command bound to Shift+Pick was set to "ADgpf_selectCenter"...
fyi: at any time to see which interactive commands are active in ADT, click on the 'hand icon'( which is the 8th from the left) in the row of ICONS at the top of ADT.

Also, I want to know what's the use of the option Grid -> Ste Maptypes -> Choose Flex residues, when are we suppose to use this option.

>>When a docking includes flexible residues, a grid map must be created for each atom type in the ligand AND for any atom types in flexible residues that are not also in the ligand. SO, if the flexible residues have some atom types that are not also in the ligand, they must be also be specified in the gpf....
   
    Best wishes,
       Ruth

Thanks in advance for help
---------Monu
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