Re: [AMBER] Patches Installation Failure

From: Jason Swails <>
Date: Wed, 24 Sep 2014 07:52:28 -0400

On Wed, 2014-09-24 at 16:42 +0800, 张后今 wrote:
> Hi, guys:
> I am new to Amber. When using amber-update to install the patches, it
> encounters some problems with patch No.2. The update stops there and
> the program exits. Is this a bug for amber14?

It's possible, but you gave so little information that it's impossible
to tell. I have never seen this fail before. By contrast, there are
_many_ ways that you can see this error that do not indicate a problem
with Amber at all:

1. You partially copied an already-patched version of Amber 14 from
another source but didn't copy the .patches folder.
2. For some reason you removed the .patches folder or some of the files
3. You modified one of the same files that update.2 modifies, so
update_amber could no longer figure out _how_ to apply this update.
4. You pointed update_amber to the wrong mirror to download updates

Hopefully the only ones that should reasonably apply to you are 1 or 3
(the others are equivalent to taking a sledgehammer to update_amber :).
It could also be that the update you refer to happens not to work on a
particular platform (like Cygwin). That happened with AmberTools 13 and
a workaround had to be found.

Try to start with a fresh copy of AmberTools 14 (fresh from the tarball)
and try to install from there. If you are still encountering the same
problems, I would need to be able to reproduce the problem in order to
diagnose what is happening (which means I need to know what operating
system you're using as well as any other pertinent information).

> How could I bypass patch No.2 and install the remaining patches?

You can't.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Wed Sep 24 2014 - 05:00:02 PDT
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