this is fine, this "bond" is used because the TIP3P
water model is rigid.
----- Original Message -----
From: <jz7.duke.edu>
To: <amber.scripps.edu>
Sent: Monday, June 28, 2004 1:34 PM
Subject: AMBER: question about water molecule
> Dear all,
>
> I have a question about the water molecule. I am using xleap to build the
> prmtop file and inpcrd file. I use TP3 for the crystal water molecule, and
> add waterbox around my system. When I type "edit **" and visualize the
> whol system, I found that there is a bond between the two H's of the water
> molecule. Is there anything wrong with the parm file or my input file? Why
> is there an extra bond?
>
> Thanks a lot!
>
> Best,
> Jeny
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Received on Mon Jun 28 2004 - 18:53:00 PDT
