Re: [AMBER] amber installation on linux mint

From: nahoum a via AMBER <>
Date: Fri, 13 Jan 2023 11:22:44 +0000

I've made progress in my installation of Amber22, but the make install step still fails. Based on David Case's recommandations, I've installed zlib and libbz2 from source myself, using "./configure prefix=/tank/amber/amber/amber22/amb22_inst/lib/zlib" before "make install" for zlib, and "make install PREFIX=/tank/amber/amber/amber22/amb22_inst/lib/libbz2" for libbz2

Prior to my latest attempt, in the amber22_src/build directory, I've run "make clean", then "./clean_build". I then went "./run_cmake", which successfully installed miniconda, and completed without error messages, and "make install", which reached ~25%, before exiting with the following

common.copy /tank/amber/amber/amber22/amber22_src/build/AmberTools/src/boost/stage/lib/libboost_thread.a
gcc.compile.c++ /tank/amber/amber/amber22/amber22_src/build/AmberTools/src/boost/build/boost/bin.v2/libs/timer/build/gcc-ambercmake/debug/link-static/threading-multi/auto_timers_construction.o
gcc.compile.c++ /tank/amber/amber/amber22/amber22_src/build/AmberTools/src/boost/build/boost/bin.v2/libs/timer/build/gcc-ambercmake/debug/link-static/threading-multi/cpu_timer.o
gcc.archive /tank/amber/amber/amber22/amber22_src/build/AmberTools/src/boost/build/boost/bin.v2/libs/timer/build/gcc-ambercmake/debug/link-static/threading-multi/libboost_timer.a
common.copy /tank/amber/amber/amber22/amber22_src/build/AmberTools/src/boost/stage/lib/libboost_timer.a
...failed updating 5 targets...
...skipped 3 targets...
...updated 115 targets...
AmberTools/src/boost/CMakeFiles/boost_build.dir/build.make:93: recipe for target 'AmberTools/src/boost/Stamp/boost_build/boost_build-build' failed
make[2]: *** [AmberTools/src/boost/Stamp/boost_build/boost_build-build] Error 1
CMakeFiles/Makefile2:4153: recipe for target 'AmberTools/src/boost/CMakeFiles/boost_build.dir/all' failed
make[1]: *** [AmberTools/src/boost/CMakeFiles/boost_build.dir/all] Error 2
Makefile:155: recipe for target 'all' failed
make: *** [all] Error 2

Please let me know if I should supply more information at this stage, and apologies to David Case for using the wrong communication channels !

Many thanks for your help so far,

Nahoum Anthony

From: David A Case <>
Sent: Thursday, January 12, 2023 10:11 PM
To: nahoum a <>
Subject: Re: [AMBER] amber installation on linux mint

On Thu, Jan 12, 2023, nahoum a wrote:
>Dear David,

Please send amber-related questions to the mail reflector,,
and not to me personally. That way, many people can see your question and try
to help, and the answers can help others with similar questions. See for information on how to
>I've finally managed to get ./run_cmake without exiting with errors. In
>order to do this, I've added directories that contained zlib.h, zconf.h,
>and to my PATH.

Doing this "by hand" seems a poor choice. If you are using any of the
standard Linux distros (or something related to them), look at the
instruction pages here: This gives
instructions on how to install all the needed packages.

Linux Mint is a variant of Ubuntu, so follow those instructions.


>/tank/amber/amber/amber22/amber22_src/AmberTools/src/cpptraj/src/tng/tng_io.c:31:10: fatal error: zlib.h: No such file or directory
> 31 | #include <zlib.h>
> | ^~~~~~~~

You don't have zlib installed correctly.

David A. Case                         |
Dept. of Chemistry & Chemical Biology |
Rutgers University                    |   skype:              dacase
174 Frelinghuysen Road, Rm. 208b      |   cell:      +1-609-751-8668
Piscataway, NJ 08854        USA       |   web:
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Received on Fri Jan 13 2023 - 03:30:02 PST
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