Re: [AMBER] Error installing amber macOS M1

From: Rodrigo da Silva Bitzer <>
Date: Tue, 28 Sep 2021 17:55:55 +0000

Dear David,
Thak you very much for your reply.

After paying careful attention to the update process, I have observed that update.1 has constantly failed. Please take a look the message below:

$ ./update_amber --update
Preparing to apply updates... please wait.
Downloading updates for AmberTools 21
Downloading AmberTools 21/update.1 (4.51 KB)
Applying AmberTools 21/update.1
/Users/rodrigobitzer/Documents/RESEARCH/MD/amber/amber20_src/updateutils/ PatchingWarning: Previously applied patch detected. Skipping.
Downloading AmberTools 21/update.2 (3.09 KB)
Applying AmberTools 21/update.2

Do you know how can I fix it?

Thank you in advance

Rodrigo S. Bitzer
Professor Adjunto A (Assistant Professor)
Molecular Modeling, Computational Catalysis and Supramolecular Chemistry
Departamento de Físico-Química, Instituto de Química
Universidade Federal do Rio de Janeiro, Brazil;
From: David A Case <>
Sent: Friday, September 24, 2021 10:04 PM
To: AMBER Mailing List <>
Subject: Re: [AMBER] Error installing amber macOS M1
On Fri, Sep 24, 2021, Rodrigo da Silva Bitzer wrote:
>I have just redownloaded both AmberTools and Amber and applied (by hand)
>the patches before running cmake. Unfortunately, the error messages
>persist.  Please find attached my cmake.log file.
I'm pretty much out of ideas...maybe someone else on the list can see what
is going on.
>>I have found the following error while running make install:
>>  124 |     namelist /sebomd/ hamiltonian, &
Somehow, you need to debug this really carefully.  Look at line 124 in the
original files (before running update_amber).  Is it the line listed above?
Then, run update_amber --update, and pay careful attention to the output,
looking for any evidence that the updating process failed for update.1.
Look at line 124 *after* the update step?  Has it changed?  Is there a file
ending in ".rej" in that directory?
Possible problems:  you don't have a proper internet connection to get the
updates;  the "patch" program on your machine is missing, or not working
somehow; something is wrong with permissions that prevents the patches from
actually being carried out; ....(??)
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Received on Tue Sep 28 2021 - 11:00:02 PDT
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