Re: [AMBER] Amber updates brings duplicate patch

From: David A Case <>
Date: Thu, 21 Nov 2019 08:29:41 -0500

On Thu, Nov 21, 2019, viktor drobot wrote:

>My patch version is 2.7.6. Re-checked on pure tarball:
>[viktor.desolve-lab /tmp]$ md5sum AmberTools19.tar.bz2
>afffe8a5473a0bd143b98f0396f52f0f  AmberTools19.tar.bz2

Above is correct.

>[viktor.desolve-lab /tmp/amber18]$ patch -p0 < update.8


>patching file test/middle-scheme/QMMM_Constr_ALA_Methol/qmmm.rst
>*Not deleting file test/middle-scheme/QMMM_Constr_ALA_Methol/qmmm.rst as
>content differs from patch*

Adding/deleting and moving files is problematic with patch. And working
with binary files is also a pain. I'm hoping to convince Jason to
support a change in the way we do things for the 2020 release.

Thanks for looking into this. Good news is that you can definitely
ignore the problem.

[Aside: we definitely check that patches apply cleanly before posting
them. But /usr/bin/patch on OSX is still at version 2.5.8, and I'm
guessing that was used to check update.8. When I run version 2.7.1, I
see the message you are seeing. So the problem indeed arises from the
fact that our update-creation instructions don't specify which version
of patch to use.]


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Received on Thu Nov 21 2019 - 05:30:04 PST
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