AMBER Archive (2009)

Subject: [AMBER] How to find water-mediated hydrogen bond?

From: Catein Catherine (askamber23_at_hotmail.com)
Date: Wed Sep 02 2009 - 09:10:37 CDT

Dear All amber users,

 

How to identify a water mediated hydrogen bond? Using ptraj, I listed out all possible hydrogen bond around drug binding site. I found

 

drug-OH...solvent 80% 2.7A...

 

solvent....HO-residueX 40% 3.0A...

 

However, how can I reconfirm the water-mediated hydrogen bond is in fact

 

drug-OH...solvent...HO-residueX

 

Or just the drug and residueX are link to different solvent molecules?

 

Best regards,

Cat

 

 

 

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