Re: [AMBER] Charmm-gui conversion

From: mohammad r <>
Date: Fri, 11 Dec 2015 15:30:06 +0000 (UTC)

Sorry I thought it is a problem.
Thank you very much.

    On Friday, December 11, 2015 5:11 PM, Jason Swails <> wrote:

 On Fri, Dec 11, 2015 at 7:39 AM, mohammad r <>

> Thank you Jason,
> I used for conversion. Now when I want to save
> parameter files in tleap, it adds hydrogen to the water molecules so when
> visualizing with vmd the water molecules are in triangular shape like the
> image I attached.

​It's unclear to me whether you think this triangular shape is a problem or
not.  To remove confusion, this is not a problem.  It's actually expected.
TIPnP water is defined using 3 distances (O-H1, O-H2, and H1-H2), rather
than the two O-H distances and an angle.  These are rigid water molecules,
which means that all 3 distances need to be held fixed via SHAKE (or
SETTLE, as is more commonly used for water).


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Fri Dec 11 2015 - 08:00:05 PST
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