Re: [AMBER] solvatebox

From: case <>
Date: Sat, 6 Nov 2010 22:14:33 -0400

On Sat, Nov 06, 2010, John S wrote:
> I used solvatebox command as follows:
> solvatebox resname MEOHBOX 0
> Since I want a periodic boundary condition with no space between the
> structure and the periodic box.

I don't understand what it is you want. The command above won't add any
methanol molecules, which is correct if you want "no space" between the solute
and box boundary. So why issue the solvatebox command in the first place?

Note that Amber is not set up for small periodic systems: the length of each
dimension of the box must be at least twice the non-bonded cutoff (plus a bit
for a buffer region). In practice this means that the minimum box dimension
is around 18-20 Ang. Of course, I don't know how big "resname" is, but you
seem to be asking for something very odd.


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Received on Sat Nov 06 2010 - 19:30:04 PDT
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