Re: [AMBER] X11 problems on Mac OS X 10.8

From: Julio Dominguez <>
Date: Tue, 2 Oct 2012 22:09:29 +0000

After running the ./ --patch-level I get.

Latest patch applied to AmberTools12: 24Latest patch applied to Amber12: 11
What I get during patch application is this:
Applying AmberTools12 patches Moving bugfix.1 to AmberTools_Applied_PatchesCreating file /Volumes/Kimahri/AMBER/amber12/AmberTools/test/cpptraj/Test_Closest/closestmols.dat Moving bugfix.2 to AmberTools_Applied_PatchesThis patch patches I will quit after this patch so the rest may be applied with the updated version. Moving bugfix.3 to AmberTools_Applied_PatchesERROR: the X11 extensions headers are not in the usual location! To search for them try the command: locate X11/extensions On new Fedora OSes install libXext-devel On RedHat OSes install libXext-devel To build Amber without XLEaP, re-run configure with '-no-X11: ./configure -no-X11 intelConfigure failed due to the errors above!
I get no other warning.
After reading your last message I ran:
./ --update-tree
several times just to be sure but I ended up having the same error:
icc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -c -o xTank.o xTank.cxTank.c(62): catastrophic error: cannot open source file "X11/IntrinsicP.h" #include <X11/IntrinsicP.h>
Any suggestions?

> Message: 8
> Date: Mon, 1 Oct 2012 19:14:17 -0400
> From: Jason Swails <>
> Subject: Re: [AMBER] X11 problems on Mac OS X 10.8
> To: AMBER Mailing List <>
> Message-ID:
> <>
> Content-Type: text/plain; charset=ISO-8859-1
> What does
> ./ --patch-level
> return when you are in AMBERHOME?
> Particularly, bugfix.23 for AmberTools 12 fixes the configure script to
> work with Mac OS X 10.8 so xleap builds (in addition to updating configure
> for the GPU update). Make sure all updates are applied.
> HTH,
> Jason

AMBER mailing list
Received on Tue Oct 02 2012 - 15:30:02 PDT
Custom Search