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PostPosted: Sat Mar 06, 2010 12:04 pm 
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Joined: Sat Mar 06, 2010 11:54 am
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Hi auto dock users.

I needed ur help regarding above mentioned topic.

As we see sometimes proteins are crystallized with few molecules of water. but when we do protein preparation for docking we remove those water molecules. If these water molecules are present in Active site by removing them we introduce majorly two type of changes:-
1. We increase the space for atoms.
2. as water contains two donors and one acceptor we make change in charges.

So is there any method by which we can define/specify the position of these co crystallized water molecules in our input files for auto dock or in any module of auto dock.


I want to retain these water molecules for my docking studies how can i accomplish this task?


Thanks in advance :)


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