Re: [AMBER] Amber 20 installation, problems with the testing phase

From: Beatriz Gomes Guimaraes <>
Date: Thu, 7 Jan 2021 21:41:27 +0000

Dear Dr Case,
Thank you for your comments.
True, I hadn't mentioned "sudo", I didn't imagine it was related ...
I will then redo the installation in the home directory to avoid any problems.
Thanks a lot again !

Beatriz Guimar„es
Laboratory of Structural Biology and Protein Engineering
Instituto Carlos Chagas - ICC / FIOCRUZ ParanŠ
Rua Prof. Algacyr Munhoz Mader, 3775 Bloco C
CIC 81350-010
Curitiba - PR, Brasil

De: David A Case <>
Enviado: quinta-feira, 7 de janeiro de 2021 17:44
Para: AMBER Mailing List <>
Assunto: Re: [AMBER] Amber 20 installation, problems with the testing phase

On Thu, Jan 07, 2021, Beatriz Gomes Guimaraes wrote:
>Updating my testing problem ...
>I tried to run make test.serial as root (after setting the AMBERHOME
>environment variable in the /root/.bashrc file) and it worked.
>I did the installation as superuser (but not root) and using "sudo make
>test.serial" (AMBERHOME environment variable in /etc/bash.bashrc) I was
>encountering the problems described in my previous messages.

Here's what is going on: if you run "sudo" it creates a new shell, and
doesn't pick up all the environment variables you have. Hence, it looks
like your AMBERHOME variable is fine, but as soon as you do anything with
sudo, you've lost the AMBERHOME variable, which is exactly what was
happening in your earlier post.

We really encourage users *not* to install with either sudo or root. You
are just taking too big a chance that (a) there is a bug in our installation
scripts; or (b) you type something wrong by accident.

If you really, really need to install the code in a protected place like
/usr/local, you may need to use superuser privileges. But think hard about
just installing in your home directory, or somewhere else where you have
write privileges, and avoid root or sudo.

Glad you found the solution! You didn't mention "sudo" in the earlier post,
and I didn't think to ask.


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Received on Thu Jan 07 2021 - 14:00:03 PST
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