Dear Sir/Madam,
I look up the archive, seems to me that you may need the config.h and g++ version to help users to installed amber on ubuntu. So, I attached my config.h file and g++ version with this email.
Hope you could give me some hints how to solve this problem. Many thanks in advanced.
>g++ version
g++: version: No such file or directory
g++: no input files
=========================config.h=======================================
# AmberTools configuration file, created with: ./configure_at gcc
###############################################################################
# (1) Location of the installation
BINDIR=/home/annie/Amber10/amber10/bin
LIBDIR=/home/annie/Amber10/amber10/lib
INCDIR=/home/annie/Amber10/amber10/include
DATDIR=/home/annie/Amber10/amber10/dat
NABHOME=/home/annie/Amber10/amber10/dat
###############################################################################
# (2) If you want to search additional libraries by default, add them
# to the FLIBS variable here. (External libraries can also be linked into
# NAB programs simply by including them on the command line; libraries
# included in FLIBS are always searched.)
FLIBS= $(LIBDIR)/libsym.a $(LIBDIR)/arpack.a $(LIBDIR)/lapack.a $(LIBDIR)/blas.a $(LIBDIR)/f2c.a
###############################################################################
# (3) Modify any of the following if you need to change, e.g. to use gcc
# rather than cc, etc.
SHELL=/bin/sh
# Set the C compiler, etc.
# For GNU: CC-->gcc; LEX-->flex; YACC-->bison -y -t;
# Note: If your lexer is "really" flex, you need to set
# LEX=flex below. For example, on many linux distributions,
# /usr/bin/lex is really just a pointer to /usr/bin/flex,
# so LEX=flex is necessary. In general, gcc seems to need
# flex.
CC=gcc
CXX=g++
CPLUSPLUS=g++
CFLAGS= -m32 -DBINTRAJ $(AMBERBUILDFLAGS)
OCFLAGS=-O3 -m32 -DBINTRAJ $(AMBERBUILDFLAGS)
NABFLAGS=
LDFLAGS=
LEX= flex
YACC= $(BINDIR)/yacc
AR= ar rv
M4= m4
RANLIB=ranlib
# Set the C-preprocessor. Code for a small preprocessor is in
# uccp-1.3; it gets installed as $(BINDIR)/ucpp;
# this can generally be used (maybe not on 64-bit machines like altix).
CPP= $(BINDIR)/ucpp -l
# These variables control whether we will use compiled versions of BLAS
# and LAPACK (which are generally slower), or whether those libraries are
# already available (presumably in an optimized form).
LAPACK=install
BLAS=install
F2C=install
# These variables determine whether builtin versions of certain components
# can be used, or whether we need to compile our own versions.
UCPP=install
C9XCOMPLEX=skip
# For Windows/cygwin, set SFX to ".exe"; for Unix/Linux leave it empty:
SFX=
# Information about Fortran compilation:
FC= gfortran
FFLAGS= -O1 -fno-automatic $(LOCALFLAGS) $(AMBERBUILDFLAGS)
FREEFORMAT_FLAG= -ffree-form
LM=-lm
BUILD_SLEAP=install_sleap
XHOME= /usr/X11R6
XLIBS= -L/usr/X11R6/lib
MAKE_XLEAP=skip_xleap
NETCDF=netcdf.mod
NETCDFLIB=../netcdf/lib/libnetcdf.a
G77=noG77
# default rules for Fortran and C compilation:
.f.o:
$(FC) -c $(FFLAGS) -o $. $<
.c.o:
$(CC) -c $(CFLAGS) -o $. $<
=======================================================================
By the way, I am using T410 thinkpad notebook with intel core i5-520M 2.4 GHz CPU.
Many many thanks for your advices.
Cat
> From: askamber23.hotmail.com
> To: amber.ambermd.org
> Date: Mon, 7 Jun 2010 16:43:31 +0800
> Subject: [AMBER] Error installing AMBER 10 on ubuntu
>
>
> 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 - 02:00:07 PDT
