Re: [AMBER] Amber Install

From: Jason Swails <>
Date: Wed, 4 Sep 2013 15:04:36 -0400

On Wed, Sep 4, 2013 at 1:45 PM, Lindsay Morrison <>wrote:

> Hi, I am trying to install Amber12 on a windows/cygwin environment. I am
> able to extract both Amber12 and AmberTools13 without any problems,
> following the instructions on
> All of
> the
> updates have been properly downloaded as well. However, I start running
> into problem when I try to run the ./ --update-tree.

I fixed that typo now, but was replaced with update_amber in
AmberTools 13. Running configure should be enough to pull in all patches,
but you need to do something special for Cygwin to get all of the patches
to work:

./update_amber --apply

(Instructions here:

For some
> reason, it can't find the script. I have tried going forward with the
> install without this step (running ./configure gnu) and the configure step
> seems to work fine. However when I run make install it eventually shoots
> back the following error message:

You should configure with the -cygwin flag.

./configure -cygwin gnu

I will also add this to the instructions.

Good luck,

Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Wed Sep 04 2013 - 12:30:02 PDT
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