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

From: Hopkins, Robert <>
Date: Tue, 11 Dec 2007 17:50:17 -0600

Dear Dr. Case and Amber Users,

Here's one final note for this thread. I just reinstalled Amber9
very successfully and also found that the patch command using the
the intact bugfix.all file worked beautifully, with one minor
exception: the next-to-last bugfix in the file -- for:
        src/sander/runmd.f *** 814, 820 *** --- 814, 825 ---
apparently failed because the 'add line' flags (+) for the proposed
changes seem to be missing. Thanks again for your comments.

Bob Hopkins

-----Original Message-----
From: Hopkins, Robert
Sent: Sunday, December 09, 2007 3:45 PM
To: ''
Subject: Re: AMBER: Installing Amber9 in a Cygwin environment on a
MS-Windows XP machine

Dear Dr. Case,

Thank you for your comments. It has taken me awhile, but I've now gone
back and reconstructed pieces from the problems with my installation of
Amber9. Mistake 1): I originally had defined the AMBERHOME environment
variable in the Cygwin.bat file as a DOS command (with the apparent
misunderstanding that Cygwin would translate it to the POSIX format
as it does for the PATH variable). Upon running the configure command,
however, and finding a mixed path in config.h, I recognized the problem
and moved the AMBERHOME definition to the Cygwin environment. So, now I
needed to edit the mixed DOS/POSIX path in config.h. Mistake 2): Being
new to Linux/UNIX, new to Cygwin and new to Amber, I used Windows Word
Pad as a text editor. BUT, not all text editors are equal, despite
identical-looking output files. As you, no doubt, already know, line
terminations in Windows/DOS consist of both a carriage return (\r) and a
newline (\n), whereas Linux/UNIX uses only a newline (\n) for this
purpose. Both bash and Bourne shells have a problem with \r, but there
seemed to be no problem changing to ash, so I did. Thus, I'm now
planning to re-install Amber9 (a bit older and a bit wiser) -- I'll have

a chance to check on the behavior of patch with bugfix.all at that time.

Recommendations to other newbies trying to install Amber9 in a Cygwin
environment like me: a.) be sure to define the AMBERHOME environment
variable *within* the Cygwin environment, and b.) use *only*
Linux/UNIX-friendly text word processors like, for example, vi or emacs.
I would reiterate Dr. Case's final point: *first* try things as stated
in the instructions (if you aren't part of the solution, you're probably
part of the problem)!

Bob Hopkins

-----Original Message-----
From: [] On Behalf
Of David A. Case
Sent: Tuesday, November 13, 2007 9:55 AM
Subject: [Subject Filtered] Re: AMBER: Installing Amber9 in a Cygwin
environment on a MS-Windows XP machine 7%

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

> After searching the Amber Mailing List Archives, I didn't find
> 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,
> that it might save others a few frustrations.

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

> 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
> 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
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
> 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


The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Wed Dec 12 2007 - 06:07:35 PST
Custom Search