Re: [AMBER] issue while installing AMBER tools on windows10 Linux subsystem

From: Gustaf Olsson <>
Date: Fri, 20 Mar 2020 22:49:39 +0000

Hello Ana

So, the shell and path issues can be overwhelming in the beginning. If you have not switched shells and you are in the WSL then you are using bash, 100%. The the "setenv" should fail as this is a "csh/tcsh" specific command.

This command:

    test -f /home/maryam/amber18/amber.csh && source /home/maryam/amber18/amber.csh (csh/tcsh)

Should not be executed!

This command:

sudo echo "test -f /home/[username]/amber18// && source /home/[username]/amber18//" >> ~/.bashrc

Is the only one you should run, as is with no other arguments. For you this means:

sudo echo "test -f /home/maryam/amber18// && source /home/maryam/amber18//" >> ~/.bashrc

and do NOT FORGET the:

source ~/.bashrc

If the installation worked without a problem you most likely got the "export AMBERHOME" right though in order to get the test running properly you should get the "test" part above correct.

This might be a little bit confusing and potentially not at the correct level for you though I'd like to recommend looking into the "path" and environmental variable concept:


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Best regards

// Gustaf

Från: Ana Ziad <>
Skickat: den 20 mars 2020 18:29:33
Ämne: Re: [AMBER] issue while installing AMBER tools on windows10 Linux subsystem

Dear Professor Case,
I cant fully understand the last two paragraphs of your email. The make
test is now working. I am waiting to for it end and then check if the
AMBERtools modules are working properly.

On Fri, Mar 20, 2020, Ana Ziad wrote:

>We recommend adding the line:

  test -f /home/maryam/amber18/ && source

The above is the one you need. Note that the "(sh/bash/zsh)" part is a
comment. You are almost certainly not running the csh shell (see

> test -f /home/maryam/amber18/amber.csh && source
>/home/maryam/amber18/amber.csh (csh/tcsh)

In my view, this comment causes more harm than good, and should be
removed. If there is any poor soul out there using tcsh as an
interactive shell, they almost sure know that they are doing that, and
know how to handle situations like this.

Stated in other terms: the number of users to don't know what shell they
are using (and hence are likely to be confused by this message) is far
greater than the number of people actually using tcsh (only a few of
whom would not already know this information.)


On Fri, Mar 20, 2020 at 7:50 PM Ana Ziad <> wrote:

> *Dear Gustaf,*
> *Thank you for your help.*
> *I repeated all the steps again and this time installation was successful
> but now I encountered another issue with "setenv"*
> *So this is the installation message:*
> Installation of AmberTools19 serial is complete at Fri Mar 20 19:10:02
> +0330 2020.
> *but make test didn't work:*
> make test
> make[1]: Entering directory '/home/maryam/amber18/AmberTools/test'
> ./
> Error: Could not import Amber Python modules!
> Probably your Amber Python environment was not set up correctly.
> We recommend adding the line:
> test -f /home/maryam/amber18/ && source
> /home/maryam/amber18/ (sh/bash/zsh)
> or
> test -f /home/maryam/amber18/amber.csh && source
> /home/maryam/amber18/amber.csh (csh/tcsh)
> to your login shell resource file (e.g., ~/.bashrc or ~/.cshrc).
> Makefile:8: recipe for target 'test' failed
> make[1]: *** [test] Error 1
> make[1]: Leaving directory '/home/maryam/amber18/AmberTools/test'
> Makefile:68: recipe for target 'test.serial' failed
> make: [test.serial] Error 2 (ignored)
> *Then I tried:*
> test -f /home/maryam/amber18/amber.csh && source
> /home/maryam/amber18/amber.csh (csh/tcsh)
> *And the error is:*
> setenv: command not found
> setenv: command not found
> -bash: /home/maryam/amber18/amber.csh: line 14: syntax error: unexpected
> end of file
> *Now when I try to call for xleap for example:*
> xleap: command not found
> *I would appreciate any help*
> *Thanks in advance *
> On Wed, Mar 18, 2020 at 1:05 AM Ana Ziad <> wrote:
>> Dear AMBER developers,
>> I am having a confusing issue while installing AMBER tools on windows10
>> Linux subsystem.
>> I am following this guide:
>> I followed all the steps up to:
>> ./configure gnu
>> Here I get this error:
>> ./configure2: 1: ./configure2: python: not found
>> Using the AmberTools miniconda installation in
>> /home/maryam/amber18/miniconda
>> version 3.7.6
>> Obtaining the gnu compiler suite versions, e.g.:
>> /path/to/the/real/GCC -v
>> Error: /path/to/the/real/GCC could not be found!
>> Configure failed due to the errors above!
>> that I tried to fix by searching the mailing list. took me a long time
>> but still not working.
>> I have python for sure. I can find the path to it, but not sure how to
>> apply that in the config file.
>> Also tried:*./configure --with-python /path/to/your/python gnu *
>> that didnt work
>> I will appreciate any help
>> thanks a lot
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Received on Fri Mar 20 2020 - 16:00:02 PDT
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