Re: AMBER: Installing Amber9 in a Cygwin environment on a MS-Windows XP machine

From: David A. Case <>
Date: Tue, 13 Nov 2007 07:54:38 -0800

On Mon, Nov 12, 2007, Hopkins, Robert wrote:

> After searching the Amber Mailing List Archives, I didn't find anyone's
> full experience of trying to install Amber9 on a MS Windows XP system
> using the Cygwin environment. So, out of appreciation for the Amber
> professionals that provide so much support (in particular, in my case,
> Ross Walker), I summarize below (for what it's worth) my experience, so
> that it might save others a few frustrations.

Thanks for the detailed instructions. I have a few comments, based on my
Cygwin experience.

> ....when I tried to apply the bugfixes using the patch command, I
> had to first edit the file bugfix.all into separate files and run each
> one separately.

I don't think this should be necessary. I routinely use the bugfix.all
file, without change, on cygwin. So, try the instructions as written first.

> 7.) When running the configuration script, use the cygwin option:
> ./configure -cygwin g95. Afterward, be sure to look at config.h. For
> example, in this file, an environment variable was defined as:
> AMBER_SRC=C:\cygwin\usr\local\amber9/src (later on, this mixed DOS/Posix
> format proved to be a problem for me).

You should not have such mixed formats. This looks like you somehow set up the
AMBERHOME variable with backslashes, even though your email indicates that you
did not do that. You really don't want things like "C:\" in your variables,
and this never happens to me.

> 9.) After reviewing the log file, if all has gone well, go to the
> $AMBERHOME/test directory and edit a file there named dacdif as follow.
> First, save a copy of dacdif as, say, dacdif.txt. Then, in the first
> line, change the shell from sh to ash:
> #!/bin/sh -> #!/bin/ash

I have never had the need to do this. For me the test suite works without any

> For anyone new to Cygwin and Amber9, I hope this information may be of
> some value.

It should be very helpful. My advice is to first try things as in the
instructions, and if they fail, look at some of the fixes Bob lists here.


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Received on Wed Nov 14 2007 - 06:07:46 PST
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