[AMBER] Error installing AMBER 10 on ubuntu

From: Catein Catherine <askamber23.hotmail.com>
Date: Mon, 7 Jun 2010 16:43:31 +0800

Dear Sir/Madam,

I am trying to install amber 10 to a linux installed with ubuntu 9.1.

I follows the discriptions in http://www.somewhereeville.com/?p=345.

I did

>sudo apt-get update

> sudo apt-get install fort77 g++ flex csh patch

No error message was found, I also setup the paths in .bashrc and .profile. Then, I downloaded the g95-x86.deb file from the www.g95.org webpage.

>sudo dpkg -i g95-x86.deb

Then, I extract the Amber10 and amberTools files by

> sudo tar xvif amber10.tar.bz2

> sudo tar xvjf ambertools-1.2.tar.bz2

then, I try to install AMBERTools

> cd $AMBERHOME

> cd src

> sudo ./configure_at gcc,

Error Message appears in gfortran and g77 compilers. Where can I found the g77 or gfortran compilers, it seems to me that I have install them already in sudo apt-get commands above. What is the error message below means?

====================================================================
> sudo ./configure_at gcc
Setting AMBERHOME to /home/Amber10/amber10
 
Warning: the X11 libraries are not in the usual location !
    To search for them try the command: locate libXt
    On Fedora Core 5 install an xorg-x11-devel package.
    On RedHat8 install an XFree86-devel package.
    For the moment Amber will be configured not to build XLEaP.

Testing the C compiler:
      gcc -m32 -o testp testp.c
OK

Obtaining the C++ compiler version:
      g++ -v
The version is ../src/configure
4.4.1
[: 520: -lt: unexpected operator
OK

Testing the g77 compiler:
     g77 -O2 -fno-automatic -finit-local-zero -o testp testp.f
./configure_at: 538: g77: not found
./configure_at: 539: ./testp: not found
Unable to compile a Fortran program using g77 -O2 -fno-automatic -finit-local-zero

Testing the gfortran compiler:
     gfortran -O1 -fno-automatic -o testp testp.f
./configure_at: 562: gfortran: not found
./configure_at: 562: ./testp: not found
Unable to compile a Fortran program using gfortran -O1 -fno-automatic
We will be unable to compile mopac or resp

Testing flex:
OK

Configuring netcdf; (may be time-consuming)

NETCDF configure succeeded.
 
The configuration file, config.h, was successfully created.
 
The next step is to type 'make -f Makefile_at'
=======================================================================

Then,

I tried to install AMBERTools to see the consequence of the error by typing following commands.

> cd $AMBERHOME/test

> sudo pico Makefile_at

According to the www.somewhereville.com instructions. I added two lines to the Makefile_at file

AMBERHOME=/location to amber10/
export AMBERHOME

I also changed #!/bin/sh to #!/bin/bash in the $AMBERHOME/bin/mopac.sh file

As expected, error message also appeared, as the file cannot be compiled correctly (I think).

====================================================================
sudo make -f Makefile_at test
( cd nab; make test )
make[1]: Entering directory `/home/Amber10/amber10/test/nab'
=====================================================
Running test to make dna duplex:

    PASSED
=====================================================
Running Reflexive test:

    PASSED
=====================================================
Running test of hashed arrays:

    PASSED
=====================================================
Running test to compute chemical shifts
   (This tests many parts of the compiler and libraries)

    PASSED

=====================================================
Running test to do simple minimization
   (This tests the molecular mechanics interface)

    PASSED

=====================================================
Running test to do simple minimization with shake
   (This tests the molecular mechanics interface)

    PASSED

=====================================================
Running test to do simple minimization
   (This tests the generalized Born implementation)

    PASSED

=====================================================
Running test to do simple minimization
   (This tests the LCPO surface area)

    PASSED

=====================================================
Running test to do simple minimization
   (This tests the ao generalized Born implementation)

    PASSED

=====================================================
Running test to do molecular dynamics with rattle

    PASSED

=====================================================
Running test of fibre-diffraction module

    PASSED

=====================================================
Running test of randomized embedding

1c1
< radius of gyration: 7.340

---
> radius of gyration:    7.196
   FAILED (OK if gyration radius is about 7 or 8)
=====================================================
Running test to compute NAB energy of 3dfr minus waters.
Compare the NAB energy with the previously computed Amber energy:
Amber8 total energy is 5184.0880
   NAB total energy is 5184.0880
    PASSED
=====================================================
Running test to create Amber force-field description
    PASSED
=====================================================
checking the prmtop file:
    PASSED
=====================================================
Running test to compute GB Newton-Raphson and normal modes:
    PASSED
=====================================================
Running test to compute non-GB Newton-Raphson and normal modes:
    PASSED
=====================================================
Running test to create a simple mmCIF file 
    PASSED
=====================================================
Running test to do simple xmin minimization
    PASSED
=====================================================
Running test to compute GB normal modes using DSYEVD:
    PASSED
=====================================================
Running test to compute GB normal modes using DSAUPD:
    PASSED
=====================================================
Running test to compute Langevin modes:
    PASSED
=====================================================
Running test to do simple lmod optimization
1c1
< Glob. min. E         =     -122.793 kcal/mol
---
> Glob. min. E         =     -122.994 kcal/mol
   FAILED (probably OK if energy is -115 to -125)
=====================================================
Running test to do simple minimization
   (This tests the generalized Born implementation)
    PASSED
=====================================================
make[1]: Leaving directory `/home/Amber10/amber10/test/nab'
cd ptraj_rmsa && ./Run.rms
diffing rms.dat.save with rms.dat
PASSED
==============================================================
cd ptraj_rms && ./Run.rms
 
ptraj: test rms and 2drms commands
diffing rms_fit.dat.save with rms_fit.dat
PASSED
==============================================================
diffing rms_nofit.dat.save with rms_nofit.dat
PASSED
==============================================================
diffing rms2d.ps.save with rms2d.ps
PASSED
==============================================================
cd ptraj_matrix && ./Run.matrix
 
ptraj: analyze fluctuation matrices
diffing 1rrb_vac_distmat.dat.save with 1rrb_vac_distmat.dat
awk: cannot open /opt/amber10/test/ndiff.awk (No such file or directory)
possible FAILURE:  check 1rrb_vac_distmat.dat.dif
==============================================================
diffing 1rrb_vac_mwcovarmat_evecs.dat.save with 1rrb_vac_mwcovarmat_evecs.dat
awk: cannot open /opt/amber10/test/ndiff.awk (No such file or directory)
possible FAILURE:  check 1rrb_vac_mwcovarmat_evecs.dat.dif
==============================================================
diffing 1rrb_vac_distcovarmat_evecs.dat.save with 1rrb_vac_distcovarmat_evecs.dat
awk: cannot open /opt/amber10/test/ndiff.awk (No such file or directory)
possible FAILURE:  check 1rrb_vac_distcovarmat_evecs.dat.dif
==============================================================
cd antechamber/top2mol2 && ./Run.top2mol2
diffing sustiva.mol2.save with sustiva.mol2
PASSED
==============================================================
diffing dna.mol2.save with dna.mol2
PASSED
==============================================================
diffing dna_wat.mol2.save with dna_wat.mol2
PASSED
==============================================================
diffing aa.mol2.save with aa.mol2
PASSED
==============================================================
cd antechamber/database && ./Run.database
diffing total.frcmod.save with total.frcmod
PASSED
==============================================================
diffing total.prepi.save with total.prepi
PASSED
==============================================================
cd antechamber/bondtype && ./Run.bondtype
diffing ABAKOE.prepi.save with ABAKOE.prepi
PASSED
==============================================================
diffing PFPHHG02.prepi.save with PFPHHG02.prepi
PASSED
==============================================================
diffing fluorescein2.mol2.save with fluorescein2.mol2
PASSED
==============================================================
diffing fluorescein_f2.mol2.save with fluorescein_f2.mol2
PASSED
==============================================================
cd antechamber/c60 && ./Run.c60
diffing buckyball.mol2.save with buckyball.mol2
PASSED
==============================================================
diffing buckyball.gzmat.save with buckyball.gzmat
PASSED
==============================================================
diffing buckyball.jcrt.save with buckyball.jcrt
PASSED
==============================================================
diffing buckyball.prepi.save with buckyball.prepi
PASSED
==============================================================
diffing buckyball.ac.save with buckyball.ac
PASSED
==============================================================
cd antechamber/charmm && ./Run.charmm
diffing ala2.inp.save with ala2.inp
PASSED
==============================================================
diffing ala2.rtf.save with ala2.rtf
awk: cannot open /opt/amber10/test/ndiff.awk (No such file or directory)
possible FAILURE:  check ala2.rtf.dif
==============================================================
diffing ala2.prm.save with ala2.prm
possible FAILURE:  check ala2.prm.dif
==============================================================
diffing ala2_charmm.mol2.save with ala2_charmm.mol2
awk: cannot open /opt/amber10/test/ndiff.awk (No such file or directory)
possible FAILURE:  check ala2_charmm.mol2.dif
==============================================================
cd antechamber/chemokine && ./Run.1b2t
diffing 1b2t.mol2.save with 1b2t.mol2
PASSED
==============================================================
diffing 1b2t.ac.save with 1b2t.ac
PASSED
==============================================================
skipping antechamber tests that depend on mopac
(cd leap && ./Run.tleap)
AMBERHOME is set to /opt/amber10
Running leap tests on ./tleap -> ../../exe/teLeap
    building force field libraries:
        '91 ff..
./Run.tleap:  Program error in leap
make: *** [test.leap] Error 1
========================================================================
The test file stop here.  Could you mind to teach me what should I do to correct this error message?
Many thanks in advanced.
Best regards,
Cat
 		 	   		  
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Received on Mon Jun 07 2010 - 02:00:05 PDT