Re: [AMBER] Inquiry about Amber installation

From: Niel Henriksen <>
Date: Fri, 14 Oct 2011 07:36:03 -0600

Regarding this:

> chen.sugar9:~/amber11$ ./apply_bugfix.x bugfix.1to17.tar.bz2 ( this does
> not work)

I think you need to supply the full path to the bugfix.1to17.tar.bz2 file regardless
of whether it is located in your current working directory.


From: Jason Swails []
Sent: Friday, October 14, 2011 4:20 AM
To: AMBER Mailing List
Subject: Re: [AMBER] Inquiry about Amber installation

On Thu, Oct 13, 2011 at 11:21 PM, Mo Chen <> wrote:

> Dear Amber users/developers,
> I have a problem installing parallel version of amber in my machine. I was
> trying to compile amber using intel compiler and mpich2 library. And my
> procedure was shown as below:
> chen.sugar9:~$ tar xzvf amber11-06-26-2011.tgz

Does this tarball contain Amber11 + AmberTools 1.5?

> chen.sugar9:~$ cd amber11
> chen.sugar9:~$ echo $SHELL
> /bin/bash
> chen.sugar9:~$ echo "export AMBERHOME=$PWD" >> ~/.bashrc
> chen.sugar9:~$ echo "export PATH=$PATH:$AMBERHOME/bin" >> ~/.bashrc
> chen.sugar9:~$ source ~/.bashrc
> chen.sugar9:~$ wget
> chen.sugar9:~$ patch -p0 -N < bugfix.all
> chen.sugar9:~$ rm bugfix.all
> chen.sugar9:~$ cd AmberTools/src/
> chen.sugar9:~/AmberTools/src$ ./configure intel
> chen.sugar9:~/amber11/AmberTools/src$ make install
> chen.sugar9:~/amber11/AmberTools/src$ cd
> chen.sugar9:~$ cd $AMBERHOME
> chen.sugar9:~/amber11$ wget
> chen.sugar9:~/amber11$ wget
> chen.sugar9:~/amber11$ ./apply_bugfix.x bugfix.1to17.tar.bz2 ( this does
> not work)

This is way too vague. What do you mean it didn't work? What errors did
you get? Until this step works, there's really little point in going
further with the Amber 11 installation.

> chen.sugar9:~/amber11$ cd AmberTools/src/
> chen.sugar9:~/AmberTools/src$ ./configure intel
> chen.sugar9:~/amber11/AmberTools/src$ cd $AMBERHOME

After this step you should be running the script if you are
building AmberTools 1.5 + Amber11. The instructions are stated at the end
of the configure script.

> chen.sugar9:~/amber11$ cd src/
> chen.sugar9:~/amber11/src$ make serial
> chen.sugar9:~/amber11/src$ cd $AMBERHOME
> chen.sugar9:~/amber11$ cd AmberTools/src/
> chen.sugar9:~/AmberTools/src$ tar xzvf mpich2_1.3.1.orig.tar.gz
> chen.sugar9:~/AmberTools/src$ ./configure_mpich2 intel
> chen.sugar9:~/amber11/AmberTools/src$ ./configure -mpi intel
> chen.sugar9:~/amber11/AmberTools/src$ cd ../../src
> chen.sugar9:~/amber11/src$ make clean
> chen.sugar9:~/amber11/src$ make parallel
> Then, at the end, the error message was as below and there is no pmemd
> executable in $AMBERHOME/bin. I also tried to follow the README file in
> pmemd directory to install pmemd, but it did not work either. Could anyone
> help me with this? Many thanks!
> rism3d_opendx.f:167:0: error: unterminated #if

To me, this is indicative of a badly applied patch. Did you see any errors
applying patches? Somehow an #endif was dropped from one of the source
files, preventing the preprocessor from finishing...

My suspicion is that your tarball doesn't contain quite what you think it
contains, so you should extract a fresh copy of Amber11 and AmberTools 1.5,
then try your above sequence (but make sure you run the
script before trying to build Amber11).


Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
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Received on Fri Oct 14 2011 - 07:00:02 PDT
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