Hi
I will follow your instruction and try that
I am using cshell My script is
#!/bin/csh -f
set amber = $AMBERHOME/bin/MMPBSA.py.MPI
mpirun -np 16 $amber -O -i mmpbsa.in -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/amber.sh && source /nethome/axt651/apps/amber14/amber.sh
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 <david.case.rutgers.edu>
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 amber.sh 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/amber.sh
If you are really running the C-shell (this is actually very rare nowadays!),
type
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
https://urldefense.proofpoint.com/v2/url?u=http-3A__www.perl.com_doc_FMTEYEWTK_versus_csh.whynot&d=DgICAg&c=y2w-uYmhgFWijp_IQN0DhA&r=0Hah93XWYYBgmROOVcaccg&m=ZpVL501_Y9FJK9TKvYc5_LK4IPZerHWfMr2drmCLSAY&s=7DcZ99yKkc-YOFgDRuJU192_783z56aStUDJ3xhdjlU&e= . 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
