AMBER Archive (2008)

Subject: Re: AMBER: Amber 8 Equivalent of the Amber 5 - Edit program

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Wed Feb 06 2008 - 18:18:38 CST

> I want to make copies of the molecule such that there are
> 100 of such molecule.

You could use it to solvate itself in leap, experimenting with the box size
until you get the desired number of copies. This would probably result in a
widely-spaced array of molecules which would need dynamics runs to compact
to a reasonable box. Something like this:

> x = copy mymol
> solvatebox x mymol 500
> saveamberparm x x_top x_crd

Bill
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