Re: [AMBER] Spherical flat bottom restraint

From: David Case <>
Date: Sun, 28 May 2017 12:02:45 -0400

On Sun, May 28, 2017, M. Wong wrote:
> I want to create a spherical water droplet in vacuum that consists of 256
> water molecules. To ensure that the evaporated water molecules will come
> back, I have decided to use a flat bottom restraint. However, after reading
> the manual, it seems that such a restraint can only be achieved using NMR
> options. To create the required restraint files, I need to use the
> makeDIST_RST program, but how can I create the 7-column file required?

The makeDIST_RST code is provided in case you already have NMR distance
restraints in Diana-like format. If not, you should just directly write
the &rst namelists by hand.

However, what you probably want here is called a "cap" in Amber lingo: see
section 17.6.10 in the 2017 Amber Reference Manual.


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Received on Sun May 28 2017 - 09:30:03 PDT
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