# Re: [AMBER] how does amber calculate the water bridge fraction

From: Ming Tang <m21.tang.qut.edu.au>
Date: Fri, 11 Jun 2021 23:27:16 +0000

Hi Dan,

Thanks for your precious information. It is really helpful. I found that they present alone in some frames and present simultaneously in other frames. I can easily get the number I want in python.

Ming

-----Original Message-----
From: Daniel Roe <daniel.r.roe.gmail.com>
Sent: Saturday, 12 June 2021 3:48 AM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] how does amber calculate the water bridge fraction

Hi,

On Fri, Jun 11, 2021 at 5:47 AM Ming Tang <m21.tang.qut.edu.au> wrote:
> I am confused about how amber calculate water bridge between residues. Below to fractions are from one of my analysis. If I want to calculate the occupancy of the water bridge between 73:GLN and 100:DC, should I use 33%, (33+36)% or 36%?

So unfortunately there isn't a straightforward answer from the data you show, because there is no way to tell from the final totals if the times that 73 and 100 are bridged are the same as when 73,100, and 101 are bridged. You really need to look in the # hbonds vs time data (what gets printed to 'out') and parse the last column that lists all the bridging interactions. Then you can count when 73 and 100 are bridged and account for if/when those times overlap with 73-100-101.

I really need to add an option to record time series data for bridges but haven't gotten around to it yet...

Hope this helps,

-Dan

>
> Bridge Res 73:GLN 100:DC 101:DC 36% (fraction)
> Bridge Res 73:GLN 100:DC 33% (fraction)
>
> Thanks a lot,
> Tammy
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Received on Fri Jun 11 2021 - 16:30:02 PDT
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