Hi Jason,
Thanks for the reply. I manage to compile amber 9 and run the tests withouts
major errors on Ubuntu 10.10 32bit.
Thanks again.
On Mon, Jun 6, 2011 at 8:58 PM, Jason Swails <jason.swails.gmail.com> wrote:
> Hello,
>
> On Jun 6, 2011, at 3:17 AM, TH Chew <teonghan.gmail.com> wrote:
>
> > Greetings,
> >
> > I recently attempt to install Amber 9 on Ubuntu 11.04 64-bit. What I did:
> >
> > sudo apt-get install csh libxt-dev libxext-dev bison flex xorg-dev
> > build-essential gfortran g++
> > set AMBERHOME=/path_to_amber/
>
> AMBERHOME is an environment variable like PATH, so you should export it as
> well.
>
> > export PATH=$PATH:$AMBERHOME/exe
> > cd $AMBERHOME
> > patch -p0 -N -r patch_rejects < bugfix.all
> > cd $AMBERHOME/src
> > make serial
> > cd $AMBERHOME/test
> > make test.serial
> >
> > And this error comes out:
> >
> > ============================
> >
> > '94 ff..
> >
> > diffing ../../dat/leap/lib/all_amino94.lib with all_amino94.lib
> > PASSED
> > ==============================================================
> > diffing ../../dat/leap/lib/all_aminoct94.lib with all_aminoct94.lib
> > PASSED
> > ==============================================================
> > diffing ../../dat/leap/lib/all_aminont94.lib with all_aminont94.lib
> > PASSED
> > ==============================================================
> > diffing ../../dat/leap/lib/all_nucleic94.lib with all_nucleic94.lib
> > PASSED
> > ==============================================================
> > diffing ../../dat/leap/lib/ions94.lib with ions94.lib
> > PASSED
> > ==============================================================
> >
> > loadpdb and saveamberparm: 94 ff..
> >
> > ./Run.tleap: Program error in leap
> > make: *** [test.leap] Error 1
> > ============================
> >
> > I looked in test/ff94_prm.out and found this:
> >
> > ============================
> > -I: Adding /home/teonghan/Desktop/amber9/dat/leap/prep to search path.
> > -I: Adding /home/teonghan/Desktop/amber9/dat/leap/lib to search path.
> > -I: Adding /home/teonghan/Desktop/amber9/dat/leap/cmd to search path.
> > -I: Adding /home/teonghan/Desktop/amber9/dat/leap/parm to search path.
> > -s: Ignoring startup file: leaprc
> > -f: Source ff94_prm.cmd.
> >
> > Welcome to LEaP!
> > Sourcing: ./ff94_prm.cmd
> > Log file: ./ff94_prm.log
> > ----- Source: ../../dat/leap/cmd/leaprc.ff94
> > ----- Source of ../../dat/leap/cmd/leaprc.ff94 done
> > Log file: ./leap.log
> > Loading parameters:
> /home/teonghan/Desktop/amber9/dat/leap/parm/parm94.dat
> > Reading title:
> > PARM94 for DNA, RNA and proteins with TIP3P Water. USE SCEE=1.2 in energy
> > progs
> > Loading library: ./all_nucleic94.lib
> > Segmentation fault
>
> This was caused by bugs that only showed up in 64-bit builds. They have
> since been fixed. You can install the latest AmberTools (1.5) from the
> website and just use the tleap from there instead.
>
> HTH,
> Jason
>
> --
> 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
>
--
Regards,
THChew
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Jun 06 2011 - 22:30:02 PDT
