Hello,
See this website:
http://ambermd.org/ubuntu.html
This lists the packages that you need to install for amber to work properly
(it says amber11, but it applies for amber10 as well). Then follow the
instructions detailed in the Amber10 manual. Make sure you have AmberTools
1.2 extracted into the amber10 directory, and follow those instructions.
(Install AmberTools 1.2 first, then Amber10).
Good luck!
Jason
2010/6/9 Catein Catherine <askamber23.hotmail.com>
>
> Dear Amber administrators,
>
>
>
> I am new to install amber10 on unbunta.
>
>
>
> I wonder if I have to do "./configure gcc" and do "make -f Makefile_at",
> and then do another compilation with gfortran again with the following
> commands lines "./configure gfortran" and do "make -f clean Makefile_at"
> again to compile all the units in Amber tools?
>
>
>
> I also wonder if we should "tar xvfj AmberTools.tar.bz2" under root or sudo
> command.
>
>
>
> I know X11 library is needed to install amber on red hat linux. Do i need
> to define any library location in .bashrc when I do the installation on
> ubunta?
>
>
>
> Attached is the ./config.h file I created with ./configure gcc only.
> However, I tried many times, the sleap tests still have error that "find
> not found" (all other tests are OK). I am wondering if I have not compile
> the sleap properly with the right compiler or I should not extract the files
> as a root or I did not define the necessary library correctly.
>
>
>
> Pls kindly help. Many thanks in advance.
>
>
>
> Best regards,
>
>
>
> Cat
>
> ========================================================================================================
> >
> > # 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=install_xleap
> >
> > NETCDF=netcdf.mod
> > NETCDFLIB=../netcdf/lib/libnetcdf.a
> > G77=hasG77
> >
> > # default rules for Fortran and C compilation:
> >
> > .f.o:
> > $(FC) -c $(FFLAGS) -o $. $<
> >
> > .c.o:
> > $(CC) -c $(CFLAGS) -o $. $<
> >
> > ~
> > ~
> >
> ===============================================================================================================
> >
> >
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>
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Wed Jun 09 2010 - 09:00:06 PDT
