Re: [AMBER] numpy related problem in amber

From: Elvis Martis <>
Date: Thu, 6 Dec 2018 04:52:32 +0000

Try using "which sander" (without quotes) and you know if the environments variables are correct.
#export AMBERHOME=/home/biopo5/Downloads/amber18
Since you have used # the bash cannot read this line, remove the # and it should be fine.

Best Regards
Elvis A F Martis
Molecular Simulations Group,
Department of Pharmaceutical Chemistry,
Bombay College of Pharmacy,
Kalina, Santacruz [E],
Mumbai 400098,
Institute Web-address:
Research Group Web-address:
Personal Web-address:

From: Seketoulie Keretsu <>
Sent: 06 December 2018 09:35
Subject: [AMBER] numpy related problem in amber

Dear Expert,

I am fairly new to linux and amber18 environment. I have recently
installed the amber18 package (successly). It seems like numpy is
correctly installed but cannot be detected. I assume it could be due
to problem related to PATH. Please correct me if I am wrong.

Amber was installed in : /home/biopo5/Downloads/amber18
>echo $PATH

As per some online searches i have added some line to the .bashrc file
(shown below)

# .bashrc
# Source global definitions
if [ -f /etc/bashrc ]; then
        . /etc/bashrc
# Uncomment the following line if you don't like systemctl's auto-paging featur$

# User specific aliases and functions
export PATH=$PATH:/usr/local/gromacs/bin
#export AMBERHOME=/home/biopo5/Downloads/amber18
test -f /home/main/Downloads/amber18/ && source /home/main/Downloads/am$

I am not sure if the PATH are correctly added, please advise regarding
my PATH to add amber properly. Also numpy was supposed to be installed
(as per ./configure of amber) why do i still get the "ImportError: No
module named numpy". Please advise.

Thank you.


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Received on Wed Dec 05 2018 - 21:00:02 PST
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