Re: [AMBER] AmberTools installation issue

From: David A Case via AMBER <>
Date: Tue, 19 Jul 2022 08:48:27 -0400

On Sun, Jul 17, 2022, Rybenkov, Valentin V. via AMBER wrote:

>This is an update to the installation error of AmberTools22. I traced the
>error to a specific line in makefiles. The error involves an attempt to
>write into a privileged area. It occurs on line
>$(MAKE) $(MAKESILENT) -f CMakeFiles/Makefile2 PerlMol
>of the “# Target rules for targets named PerlMol’ of the main Makefile.
>Then into the block “# Target rules for target
>AmberTools/src/PerlMol-0.3500/CMakeFiles/PerlMol.dir” of
>Then into the file
>AmberTools/src/PerlMol-0.3500/CMakeFiles/PerlMol.dir/build.make, line “cd
>&& /usr/bin/make”,
>Specifically, the instruction “/usr/bin/make”
>generates an error, using presumably the Makefile in
>I do not understand why this script tries to write into a write-protected
>directory. This seems to be a bug in the installation package. Is there a
>way to bypass it?

Thanks for the detailed report, but I don't know why you are seeing this
problem, but no one else has reported it. There is no specific mention of
"/var" in this Makefile, and you may be correct that the C compiler is
choosing it. This is code from the Perl community, and we didn't write it.

We test Amber on CentOS 7 in a pretty vanilla virutal machine, and don't see
the problem.

Try adding the following define to your run_cmake script:


Remove the CMakeCache.txt file, and re-run the script, followed by make
install. That should skip the problem.

....hope this helps...dac

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Received on Thu Aug 04 2022 - 13:34:46 PDT
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