Re: [AMBER] Error installing amber macOS M1

From: Rodrigo da Silva Bitzer <>
Date: Tue, 28 Sep 2021 20:39:17 +0000

Dear David,

Line 124 of sebomd_module.F90 before applying updates (.tar.bz2 files just downloaded):
124 namelist /sebomd/ hamiltonian, &

Line 124 after running update_amber --update
124 namelist /sebomd/ hamiltonian, & (no changes!)

The error message below was found only for update.1 during update_amber --update:
/Users/rodrigobitzer/Documents/RESEARCH/MD/amber/amber20_src/updateutils/ PatchingWarning: Previously applied patch detected. Skipping.

I have tried your proposed procedure and it did not work, giving a strange error message:
% pwd
% patch -p0 < update.1
patch: **** out of memory

(I cannot understand this out of memory error!)

I really do not think update.1 has been previously applied, since the errors persist even when I use freshly downloaded files.

Thank you for your support!

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: Tuesday, September 28, 2021 5:00 PM
To: AMBER Mailing List <>
Subject: Re: [AMBER] Error installing amber macOS M1
On Tue, Sep 28, 2021, Rodrigo da Silva Bitzer wrote:
>After paying careful attention to the update process, I have observed
>that update.1 has constantly failed. Please take a look the message
>$ ./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.
>  PatchingWarning)
>Downloading AmberTools 21/update.2 (3.09 KB)
What is in line 124 of sebomd_module.F90?  Are there any other similar
warnings about other updates?  Is there any chance that the message above is
correct, i.e. that somehow update.1 had already been applied?
Here's a test I did:
1.  download update.1 from
2.  untar the Amber21.tar.bz2
     cd amber20_src/AmberTools/src/sander
       (look at line 124 of sebomd_module.F90)
     cd ../../..
     patch -p0 < update.1
     cd AmberTools/src/sander
       (look at line 124 of sebomd_module.F90)
I got no errors from the patch command, and line 124 indeed was changed by it.
If possible, you might try to install and update AmberTools21 on a different
computer, just to see if that might provide any clues.
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Received on Tue Sep 28 2021 - 14:00:02 PDT
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