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
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Received on Mon Jun 06 2011 - 06:00:02 PDT
