AMBER Archive (2005)

Subject: Re: AMBER: How to simulate a crystal structure?

From: Joseph Nachman (nachman_at_hera.med.utoronto.ca)
Date: Wed Oct 12 2005 - 11:57:56 CDT

You also have to generate and add manually the symmetry mates of you
molecule. E.g. for space group P2(1), you have to add to your initial
coordinates, those of the molecule related by the 2-fold screw axis, and
possibly translate it back into the unit cell.

Hope this helps,

Joseph

On Wed, 12 Oct 2005, David A. Case wrote:

> On Tue, Oct 11, 2005, Chunhu Tan wrote:
> >
> > I want to simulate a crystal structure, but its unit cell is not
> > rectangular ( Beta \= 90). So, can I set such a box in Leap and run a
> > simulation with PMEMD? If yes, how to do that?
>
> It is possible to do crystal simulations of unit cells, but you have to do a
> lot "by hand", since LEaP does not automate this process.
>
> First, you need to construct initial coordinates. This is not trivial, since
> typically many solvent molecules are missing from X-ray structures, and these
> have to be filled in, but you don't know in advance how many there are, or
> where they should be.
>
> Second, you would just edit the final line of the inpcrd file to put in the
> unit cell dimensions and angles that you want.
>
> This is not a task for a novice. Maybe other readers of the list will have
> some good suggestions about how to get things started. (Once you have a good
> set of initial conditions, actually carrying out the simulation is now
> different than for liquid-state simulations.)
>
> ...good luck...dac
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