I am trying to dock a small molecules on a protein and before I do that I want to remove all the water molecules from a protein structure except those participating in the catalysis. I know the active site but how can I select the water molecules that are not involved in the catalysis? Any help would be greatly appreciated. Thank you.
Dear,
Deleting water as a whole or selected molecules using ADT use steps below
(for complete deletion)
1. File >> Read Molecule >> Open your PDB file >> Edit >> Delete Water.
2. File >> Read Molecule >> Open your PDB file >> Select >> Select from String >> Click and Hold on Residue Sets in Opened Widget >> Water >> Add >> Dismiss >> Edit >> Delete >> Delete Selected Atoms.
(for Selected deletion)
3. File >> Read Molecule >> Open your PDB file >> Go to control panel >> Expand at Unit Level >> Select the Unit you want to delete >> Edit >> Delete >> Delete Selected Atoms. (Be cautious coz Undo is disabled here.)
Also you can use "Invert Selection" under "Select" smartly for such purpose. Use of Text editor is also a way to do this.
Wishes.
In Chimera:
1. Select > Structure > solvent
2. Actions > Atoms/Bonds > delete
Usually its recommendable to retain the water within 5 angstroms around the active site as these water molecules play a key role in catalysis and thermodynamic stability. Hence remove all other water molecules above 5 angstroms around active site. This can be easily done using Pymol visualization software. Moreover, we can also look at the water molecules which are interacting with the active site residues in pymol and this information can help a lot.
Hello,
I installed AutoDock4.2, and when i tried to delete water molecule using edit->delete->delete selected molecule on AutoDockTools, i got error ERROR *********************************************
Traceback (most recent call last):
File "/usr/lib/python2.7/dist-packages/ViewerFramework/VF.py", line 929, in tryto
result = command( *args, **kw )
TypeError: doit() takes exactly 1 argument (2 given)
Hi Priyanka,
I want to know how can I retain water at around 5 A in the active site while remove the others with Pymol. I was wondering If you could help me to do this.
Thanks
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