Re: [AMBER] water mediated H-Bond

From: Sangita Kachhap <>
Date: Thu, 3 Mar 2011 09:26:52 +0530 (IST)

It is formed from start.
When I load mdcrd into VMD water molecules were showing long bonds afterwords
they were fine but DNA start to show long bonds throughout and atom pair were

>> When I load processed mdcrd with new prmtop its not showing
>> structure properly there is some long bonds.
> Do the long bonds remain constant for each frame, or do they
> change to different pairs of atoms? If you had the wrong number
> of atoms in one file, I'd expect to see the first frame more
> or less normal, then following frames having more long bonds.
> As it is, it's hard to guess.
> Bill
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Sangria Carhop

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Received on Wed Mar 02 2011 - 20:00:01 PST
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