RE: AMBER: Problems with 'make'

From: Hopkins, Robert <>
Date: Fri, 5 Oct 2007 13:32:24 -0500

Thanks Ross!


Your prompt and perceptive analysis was right on. After wiping the egg
off my face, it hit me that I had been trying to proceed from the
$AMBERHOME/exe directory after I'd misinterpreted the step in the
Install Readme that says, "d. compile and install the binaries into


With your suggestions, the 'make serial' command hummed along
beautifully, creating & assembling '.o' files, up to a point. However,
the following output then came up:

            (In $AMBERHOME/src/addles):


                                    ' All apparently OK



            cd ../lib; ./Makelist: ../lib/random.o ../lib/mexit.o

            /bin/sh: ./Makelist: /bin/csh: bad interpreter: no such
file or directory

            make[1]: *** [libobj] Error 126

            make[1]: Leaving directory '/usr/local/amber9/src/addles'

            make: *** [serial] Error 2


At this point the output stopped and the prompt returned to


I looked at the Makelist file and noticed the first line reads:

            #!/bin/csh -f

It appears this should be, but might not be, interpreted as a remark.
Indeed, there is no csh program in /bin. With my limited UNIX/Linux
experience, I'm not sure if this is even relevant. Again, I'd greatly
appreciate any suggestions.


Bob Hopkins



From: [] On Behalf
Of Ross Walker
Sent: Thursday, October 04, 2007 3:55 PM
Subject: RE: AMBER: Problems with 'make'


Dear Robert,


Just to check are you in $AMBERHOME/src when you are typing make or just


In the later case you will see "make: *** No rule to make target
`serial'. Stop." because there is no makefile in the amber9 root
directory. The makefile is under the src directory so you need to do:


cd $AMBERHOME/src/

make clean

make serial


See if that works, if not and you are definately in the src directory
please check that you have a file called "Makefile" present in that


Good luck...



|\oss Walker

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| San Diego Supercomputer Center |
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        From: []
On Behalf Of Hopkins, Robert
        Sent: Thursday, October 04, 2007 12:08
        Subject: AMBER: Problems with 'make'

        Amber Users:


        I'm new to Amber and relatively new to UNIX/Linux. Nonetheless,
I'm trying to install Amber9 on a laptop running Windows XP. I've
successfully installed the Cygwin environment as well as g95. After
unpacking the Amber files, setting the environment variables & path,
applying all of the Bug fixes and running the configuration script, all
successfully, I hit a brick wall trying to 'make serial'. Although a
'make' utility was supplied with the old g77, there was none with g95,
so I installed the 'make' utility for Cygwin. However, this version
neither recognizes 'make serial' nor 'make clean' - a similar error is
reported in each case:


        make: *** No rule to make target 'serial'. Stop.


        Although I've searched the mail archives at both the Scripps and
UK Amber sites, I haven't found an answer to this problem. It may be
that I'm overlooking something, but it appears that many others have had
some type of problem with the 'make' command. I would greatly
appreciate any help or suggestions in regard to this impasse.



        Bob Hopkins


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Received on Sun Oct 07 2007 - 06:07:47 PDT
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