AMBER Archive (2004)

Subject: AMBER: question about water molecule

From: jz7_at_duke.edu
Date: Mon Jun 28 2004 - 12:34:19 CDT

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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