Re: [AMBER] make install errors

From: Hai Nguyen <>
Date: Mon, 14 Oct 2019 23:27:24 -0400

hi Alen,

What's exact commands did you specify?
You have "amber18//lib/python2.7/" folder but you say you also have
"AMBERHOME/amber18/miniconda3", which is a python3 distribution. So there
are some conflicts here.

If possible, please try again with the latest AmberTools 19 that can work
with your amber18.
I suggest to
- download the tarfile from amber website:
- open a new terminal and untar it and follow the instructions in amber
manual to compile the suite.

PS: During the installation process, I suggest to say "Yes" (again) so
Python will be installed via Miniconda.
Please record your commands + the output logs to make it easier to debug.


On Mon, Oct 14, 2019 at 10:28 PM Alen Ahmetovic <> wrote:

> Hi all,
> I am trying to install Amber and Tools18 on my PC. I am running through
> Ubuntu. When doing the installation, I keep getting stuck with the
> following error:
> make[5]: Leaving directory
> '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/cpptraj/src'
> make[4]: Leaving directory
> '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src/cpptraj'
> make[3]: Leaving directory
> '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src'
> (cd pytraj && AMBERHOME=/mnt/c/Users/Alen/Documents/Research/amber18/
> AMBER_PREFIX=/mnt/c/Users/Alen/Documents/Research/amber18/
> PYTHONPATH=/mnt/c/Users/Alen/Documents/Research/amber18//lib/python2.7/site-packages
> /mnt/c/Users/Alen/Documents/Research/amber18//bin/amber.python
> install -f --prefix=/mnt/c/Users/Alen/Documents/Research/amber18/
> --disable-openmp > build.log )
> Traceback (most recent call last):
> File "", line 18, in <module>
> from setuptools import setup, Extension
> ImportError: No module named setuptools
> Makefile:505: recipe for target 'pytraj' failed
> make[2]: *** [pytraj] Error 1
> make[2]: Leaving directory
> '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src'
> Makefile:26: recipe for target 'serial' failed
> make[1]: *** [serial] Error 2
> make[1]: Leaving directory
> '/mnt/c/Users/Alen/Documents/Research/amber18/AmberTools/src'
> Makefile:7: recipe for target 'install' failed
> make: *** [install] Error 2
> alen.DESKTOP-9902UPO:/mnt/c/Users/Alen/Documents/Research/amber18$ sudo
> apt-get install python-setuptools
> [sudo] password for alen:
> Reading package lists... Done
> Building dependency tree
> Reading state information... Done
> python-setuptools is already the newest version (20.7.0-1).
> 0 upgraded, 0 newly installed, 0 to remove and 119 not upgraded.
> then I try:
> alen.DESKTOP-9902UPO:/mnt/c/Users/Alen/Documents/Research/amber18$ python
> ./ install
> python: can't open file './': [Errno 2] No such file or directory
> I have tried to do a clean install and still get the same error. I have
> made all of the possible patch updates and relevant program downloads based
> off the errors given throughout the process, and I still end up in the same
> place. I don't have any coding experience other than what I've learned
> using Amber and copy/pasting commands I find online to fix these problems,
> otherwise I am totally lost. I added the last two commands to show that I
> have the setuptools its telling me I don't have, and the fact that asking
> it to specifically download does not work. What am I missing?
> Does setuptools need to be in the proper directory for python within amber
> to use it correctly? Currently it's in AMBERHOME/amber18/miniconda3.
> Thanks in advance for your help.
> Alen
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Received on Mon Oct 14 2019 - 20:30:02 PDT
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