Re: [AMBER] Cataline

From: Gustaf Olsson <>
Date: Mon, 14 Oct 2019 20:34:00 +0000

Hello David and Bill

Yes, the default shell for new Macs will be zsh. Changing to any other shell works still however does invoke a prompt to switch

    The default interactive shell is now zsh.
    To update your account to use zsh, please run `chsh -s /bin/zsh`.
    For more details, please visit

> Do you have a /usr/include/locale.h? As with OSX 10.14, it may be
> necessary to load a header package to get headers where they are often
> expected to be.

No, as of the last Xcode version before updating to 11 the "missing header files" were no longer included. These do not ship with Xcode any more as far as I can see. However, if I remember it correctly this was for libstdc/libstdc++ which were being deprecated and programmers encouraged to switch to libc/libc++.

Apparently, unlike csh and bash, the new mac zsh does not read the ~/.profile when starting a new session. This is where I have always placed the sourcing of before as this file was read by "all" shells. Now, I had to create the ~/.zshrc file and explicitly source the file from there. This added AMBER_PREFIX and AMBERHOME to path correctly.

I am currently compiling again to see if this takes care of the header issues and I'll update you on this tomorrow.

> $ env

Tells me, well noting about my C/C++ bindings whatsoever.

Sorry, I cannot wait for the compilation to finish before hitting the sack so I'll just have to do a cliffhanger here and get back to you once I know if getting the path variable correct affects the outcome (I did export AMBERHOME last night though not _PREFIX or the additional python references in

Otherwise I'll look into specifying the missing locale.h info manually or consult my previous notes on how I made this issue go away before.

Thank you both for your recommendations and feedback and yes, I would suggest holding of on updating macOS if you need to compile amber from source.

Best regards

// Gustaf

Från: David A Case <>
Skickat: den 14 oktober 2019 14:52:25
Till: AMBER Mailing List
Ämne: Re: [AMBER] Cataline

On Sun, Oct 13, 2019, Gustaf Olsson wrote:

>Yes, it is time to upgrade the OS on my Macs ....

Thanks for pointing out to users that OSX 10.15 (Catalina) is an
unusally disruptive update for lots of software. In particular, Amber
is not yet supported there. (Lots of other things, like 32-bit
binaries) also will no longer work. Other things got moved around, and
(I gather) the default shell is now zsh rather than bash.

>In file included from src/_rdparm.cpp:17:
>/amber18/AmberTools/src/parmed/src/readparm.h:5:10: fatal error:
> 'locale' file not found
>#include <locale>

Do you have a /usr/include/locale.h? As with OSX 10.14, it may be
necessary to load a header package to get headers where they are often
expected to be.

Disclaimer: I've not yet had time (and a spare machine) to try this
upgrade, so I'm just making guesses here.


AMBER mailing list
AMBER mailing list
Received on Mon Oct 14 2019 - 14:00:02 PDT
Custom Search