Re: [AMBER] waters in interface between protein and dna / water mediated hydrogen bonds

From: Bill Ross <ross.cgl.ucsf.EDU>
Date: Sun, 9 Jan 2011 09:53:33 -0800

> I want to obtain the number of water which are in interface between protein
> and dna.
> I also want to know exact number which every water molecule has(for example
> water : 110, 112, 245,....).
> then, I want to obtain water mediated hydrogen bonds.
> how to do that? with what tool?

ptraj is the closest to what you want.
I haven't used it, but you might have to get lists of waters
hbonded to dna and protein seperately, then find some way to
get the intersection of these lists. This could be done for
each frame..


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Received on Sun Jan 09 2011 - 10:00:04 PST
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