Re: [AMBER] ImportError: Could not import Amber Python modules

From: Thakur, Abhishek <>
Date: Thu, 17 Nov 2016 20:52:31 +0000


I will follow your instruction and try that

I am using cshell My script is

#!/bin/csh -f

set amber = $AMBERHOME/bin/

mpirun -np 16 $amber -O -i -o FINAL_RESULTS_MMPBSA.out -sp PRMT7_WT.prmtop -cp complex.prmtop -rp receptor.prmtop -lp peptide.prmtop -y *.crd

In my bashrc I have sourced it

test -f /nethome/axt651/apps/amber14/ && source /nethome/axt651/apps/amber14/

In my earlier message, the error which I have posted about bash is

bash: /nethome/axt651/apps/amber14/amber.csh: line 15: syntax error: unexpected end of file

I have got this error when I have changed my bashrc sorce with

#test -f /nethome/axt651/apps/amber14/amber.csh && source /nethome/axt651/apps/amber14/amber.csh

and the just to test I have typed bash then it gave me following bash error about sourcing amber.csh

From: David A Case <>
Sent: Thursday, November 17, 2016 9:35:53 AM
To: AMBER Mailing List
Subject: Re: [AMBER] ImportError: Could not import Amber Python modules

On Thu, Nov 17, 2016, Thakur, Abhishek wrote:

> When I did that it gave me an error

Lots of things are not getting communicated very well here. First, when
you say "I did that", *exactly* what did you type? (The and
amber.csh scripts are not marked as executable, so if you just type the
filename, you should get something like "permission denied".)
> bash: /nethome/axt651/apps/amber14/amber.csh: line 15: syntax error: unexpected end of file

More things that we don't understand. You said earlier that you were using
the C shell, but the message above is from bash. Furthermore, amber.csh is
only 8 lines long ...

My best advice: re-run the configure script, and try to follow very closely
the instructions it gives at the end: if you are indeed running bash, you
would type this:

    source /nethome/axt651/apps/amber14/

If you are really running the C-shell (this is actually very rare nowadays!),

   source /nethome/axt651/apps/amber14/amber.csh

Then proceed with the "make install" command.

...good luck...dac

[Aside: my $0.05 USD bet: there is no one under the age of 50 on
this list that uses a C-shell. So prove me wrong! Then read . Then, go ahead and change
all the Amber csh script to use /bin/sh ... :-) ]

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Received on Thu Nov 17 2016 - 13:00:05 PST
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