From owner-chemistry@ccl.net Sun Jul 22 06:35:00 2007
From: "Lukasz Cwiklik cwiklik],[gmail.com" <owner-chemistry|-|server.ccl.net>
To: CCL
Subject: CCL: Batch mode minimisation in AMBER
Message-Id: <-34777-070720200710-28538-gxeahQjuLmkszjMomR8L4A|-|server.ccl.net>
X-Original-From: "Lukasz Cwiklik" <cwiklik~!~gmail.com>
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Date: Sat, 21 Jul 2007 01:07:24 +0200
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Sent to CCL by: "Lukasz Cwiklik" [cwiklik(a)gmail.com]

On 7/18/07, David A. Case case++scripps.edu <owner-chemistry*|*ccl.net> wrote:
>
> Sent to CCL by: "David A. Case" [case/a\scripps.edu]
>
> On Wed, Jul 18, 2007, sangeeth subramaniam srdshigella---gmail.com wrote:
> >
> > Has anyone tried minimising large number of structures in AMBER.
> > I would like to know how to automate the process of minimisation in AMBER
> > for more than 500 strutcures.
>
> I think most Amber users would write a shell script (or a perl script) to
> handle a task like this.  There is also nice support for this sort of thing
> in the MMTSB toolkit (http://mmtsb.scripps.edu).
>
> There's a learning curve involved in both of these approaches, but dividends
> as well once you learn how to do it.
Hi,
If one is going to start from the beginning than maybe Python scripts
would be a good solution. Python language can be quite useful, elastic
and yet user-friendly. I have found Python scripting quite powerful
(although not always quick) tool for data analysis. But of course
David is absolutely right, shell or perl script would work as well.
Best,
Lukasz


-- 
Lukasz Cwiklik
http://cwiklik.wordpress.com


From owner-chemistry@ccl.net Sun Jul 22 19:18:01 2007
From: "David A. Case case[#]scripps.edu" <owner-chemistry,,server.ccl.net>
To: CCL
Subject: CCL: AMBER PBC box alignment
Message-Id: <-34778-070721222853-14611-HygKmlyGBw6FoQNriwRIQQ,,server.ccl.net>
X-Original-From: "David A. Case" <case++scripps.edu>
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Date: Sat, 21 Jul 2007 18:56:48 -0700
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Sent to CCL by: "David A. Case" [case:_:scripps.edu]

On Sat, Jul 21, 2007, Jun Cui juc9+]*[pitt.edu wrote:
> 
> 
> Does amber 9 need the periodic box to be parallel to the xy, yz, and xz 
> planes? 

Amber supports general triclinic unit cells, but the "a" axis must be along
the x direction, and the plane containing "a" and "b" must be in the xy plane.
(If the unit cell is a rectangular parallelopiped, this implies that box edges
are parallel to xy, yz and xz.)  I don't know of a simple code that will do
the conversion, however.

....dave case