On Fri, Dec 11, 2015 at 7:39 AM, mohammad r <mohammad.r0325.yahoo.com>
wrote:
> Thank you Jason,
>
> I used charmmlipid2amber.py 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).
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri Dec 11 2015 - 06:00:04 PST
