Re: [AMBER] [EXTERNAL] Release of AmberTools21

From: Gustaf Olsson <>
Date: Thu, 6 May 2021 12:51:29 +0000

Thank you David

I have not installed brew zlib at all, though maybe I’ll try to recompile over the weekend and se if that makes a difference.

It seems that this is connected to a prior issue with xcode which was solved by installing “deprecated” files manually:
    sudo installer -pkg /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg -target /

This is no longer possible so obviously, installing zlib and doing a bit of experimenting may be interesting.

If this does not work, it’s possible that a previous workaround "CFLAGS="-I$(xcrun --show-sdk-path)/usr/include” though pointing to the correct brew include folder may work.

If I find the time I’ll play around a bit with it and see what happens.

All the best
// Gustaf

On 6 May 2021, at 14:34, David A Case <<>> wrote:

On Thu, May 06, 2021, Gustaf Olsson wrote:

Finally had time to look at the test results of the compile, there seems to be an issue:

  ld: library not found for -lz.tbd
  collect2: error: ld returned 1 exit status

We know about this, but a solution is elusive. Once the semester is done
here in the US, we may be able to get further. Several points:

1. This only causes problems for some NAB programs. Since very few
AmberTools users use NAB anyway, for most people, this should not be a
problem. Further, many mac users actually have zlib installed via macports
or homebrew (since it is a common requirement). They should not see this

2. For a workaround, do this:

     download zlib source from<>
     ./configure; make; sudo make install
     add -DCMAKE_PREFIX_PATH=/usr/local to the run_cmake script

3. Another workaround: use the conda package, where this problem
(mysteriously) doesn't occur.

...thanks for the report....dac

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