AMBER Archive (2004)

Subject: Re: AMBER: question about water molecule

From: Carlos Simmerling (carlos_at_ilion.bio.sunysb.edu)
Date: Mon Jun 28 2004 - 12:48:11 CDT

this is fine, this "bond" is used because the TIP3P
water model is rigid.

----- Original Message -----
From: <jz7_at_duke.edu>
To: <amber_at_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
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu