Are you using sudo at all? I did notice you were installing in
/usr/local. If so, try using "sudo -e" instead of just "sudo" (to preserve
environment variables from the shell you're launching).
HTH,
Jason
On Thu, Jan 19, 2012 at 9:00 AM, Hevener, Kirk <khevener.uic.edu> wrote:
> Thanks for the advice, unfortunately I'm still getting the same error
> even after running "make distclean" in the mtkpp directory. I have also
> tried re-extracting and starting from scratch (several times), with no
> success. I know that at least one user has installed Amber in their
> home directory, could this be part of the problem? Here I'm attempting
> a system install to allow access to all users. (I do make sure
> $AMBERHOME is correctly defined when I'm attempting this installation.)
>
> Thanks,
> Kirk
>
> -----Original Message-----
> From: Jason Swails [mailto:jason.swails.gmail.com]
> Sent: Wednesday, January 18, 2012 12:38 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] AmberTools Installation Error
>
> I've never seen this issue before. It seems to be a strange compilation
> error, since it's complaining of a directory that's not really a
> directory (/include). This would happen if an environment variable was
> not set (like AMBERHOME), and the flag was -I$(AMBERHOME) or
> something...
>
> My suggestion is to go to $AMBERHOME/AmberTools/src/mtkpp/ and run "make
> distclean" to wipe out the MTK++ temporary files, then re-run configure
> making sure that $AMBERHOME is set. If that still doesn't work, try
> re-extracting both of the tarballs and starting from scratch.
>
> Good luck,
> Jason
>
> On Wed, Jan 18, 2012 at 11:59 AM, Hevener, Kirk <khevener.uic.edu>
> wrote:
>
> >
> > Dear AMBER Users:
> >
> > I'm having difficulty installing AmberTools 1.5 on an RHEL5 WS,
> > x86_64 system (2.6.18-274.12.1.el5). I can configure (serial)
> > successfully but 'make serial' throws the following error:
> >
> > libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../..
> > -I/usr/local/amber11/AmberTools/src/boost-1.38.0 -I/include -I./..
> > -DNDEBUG -DUSE_TINYXML -DTIXML_USE_STL -DC99_OK -O2 -fPIC -DHAVE_ZLIB
> > -MT gaWorld.lo -MD -MP -MF .deps/gaWorld.Tpo -c gaWorld.cpp -o
> > gaWorld.o
> > cc1plus: error: /include: not a directory
> > make[3]: *** [gaWorld.lo] Error 1
> > make[3]: Leaving directory
> `/usr/local/amber11/AmberTools/src/mtkpp/src/GA'
> > make[2]: *** [install-recursive] Error 1
> > make[2]: Leaving directory
> `/usr/local/amber11/AmberTools/src/mtkpp/src'
> > make[1]: *** [install-recursive] Error 1
> > make[1]: Leaving directory `/usr/local/amber11/AmberTools/src/mtkpp'
> > make: *** [install_mtkpp] Error 2
> >
> > This is interesting because I have successfully installed on
> > workstations very similar in our group. I have applied the latest
> > patches and set $AMBERHOME prior to configuring. What am I missing
> here?
> >
> > Thanks for any assistance,
> >
> > Kirk Hevener
> > Postdoctoral Fellow, UIC
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu Jan 19 2012 - 07:00:03 PST
