AMBER Archive (2008)

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

From: Mohd Farid Ismail (farid_at_ou.edu)
Date: Tue Mar 04 2008 - 19:09:52 CST

Thank you for the Dr. Walker and Dr. Ross for the solution. So I tried the
method and it worked well. And like Dr. Walker mentioned, it results in a
widely-spaced array of molecules. My question is, is there any command that
I can use to manipulate the location or position of the molecules. For
example a rotate or translate function in tleap to do this.

Another question is, I will need to use a constant pressure dynamics to
compress the box to the right density, right?

-Farid-

-----Original Message-----
From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
Bill Ross
Sent: Wednesday, February 06, 2008 6:19 PM
To: amber_at_scripps.edu
Subject: Re: AMBER: Amber 8 Equivalent of the Amber 5 - Edit program

> 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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