ADL: Flexible Docking

bharat lal monu46010 at yahoo.com
Mon Dec 1 20:25:12 PST 2014


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


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