Re: [AMBER] Problems of invoking the Amber 12

From: Jason Swails <jason.swails.gmail.com>
Date: Fri, 20 Dec 2013 07:02:35 -0500

On Fri, Dec 20, 2013 at 2:53 AM, Yanyan ZHU <zhuyanzily.gmail.com> wrote:

> Hi all:
> I have some puzzles as following: We have successfully installed the
> AMBER 12 in our servers, however the Amber11 was invoked in our output
> files for some computation.
> Just as "Amber 11 SANDER 2010
> PMEMD implementation of SANDER, Release 11"
>

You have to make sure that AMBERHOME points to your Amber 12 release, and
if you are just calling "sander" or "pmemd" that the Amber 12 bin/
directory appears in your PATH variable before the Amber 11 bin/ directory.


> In addition, only the Amber12 was installed in our computers .
> And for this reason, we canít successfully calculating the binding energy
> of each residue.
>

The reason you gave for your problem does not make sense.


> I want to know the reason for the problem and how to solve it.
>

You never stated what your problem was besides not being able to calculate
the binding energy of each residue (which is nowhere near enough
information for us to be able to help). Please be specific with your
problem, providing what _exactly_ you tried and the output you got from
those tries.

Also make sure that you can work through the related tutorials at
http://ambermd.org/tutorials/

Good luck,
Jason

-- 
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri Dec 20 2013 - 04:30:03 PST
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