hi Karla,
Basically you just need (in the same terminal)
source amber.sh
make install
(then drink coffee...)
After the installation is finished, open the $HOME/.bash_profile file
and add the line
test -f /Users/karlagaldamez/amber16/amber.sh && source
/Users/karlagaldamez/amber16/amber.sh
PS1: We should probably update the instruction for MacOS in this case.
PS2: If you do not have $HOME/.bash_profile, just create a new file (by any
text editor) and add the content to it.
Hope this is clear.
Hai
On Sat, Jan 21, 2017 at 2:28 AM, Karla Galdamez <kgalda.berkeley.edu> wrote:
> Hi Hai,
>
> Thank you very much for this! It all configured well utilizing the
> command: ./configure -macAccelerate clang
>
> Subsequently, I followed the instructions recommended on the output screen
> (copied below).
> I, however, copied the commands below on the screen and did not 'add' to
> startup file ( e.g. ~/.bashrc) because I do not know where the file has
> been placed. Would you be able to tell me where I can go to modify start
> up file? - Thank You!
>
>
> --------------------------------------------------------------------
> Environment resource files are provided to set the proper environment
> variables to use AMBER and AmberTools. This is required to run any Python
> programs (like MMPBSA.py, ParmEd, MCPB.py, and pytraj)
>
> If you use a Bourne shell (e.g., bash, sh, zsh, etc.), source the
> /Users/karlagaldamez/amber16/amber.sh file in your shell. Consider adding
> the line
> test -f /Users/karlagaldamez/amber16/amber.sh && source
> /Users/karlagaldamez/amber16/amber.sh
> to your startup file (e.g., ~/.bashrc)
>
> If you use a C shell (e.g., csh, tcsh), source the
> /Users/karlagaldamez/amber16/amber.csh file in your shell. Consider adding
> the line
> test -f /Users/karlagaldamez/amber16/amber.csh && source
> /Users/karlagaldamez/amber16/amber.csh
> to your startup file (e.g., ~/.cshrc)
>
> (You need to do the above before running 'make install')
>
> On Fri, Jan 20, 2017 at 9:58 PM, Hai Nguyen <nhai.qn.gmail.com> wrote:
>
> > can you try to follow the instruction here for MacOS?
> > http://ambermd.org/amber_install.html
> >
> > Basically:
> > ./configure -macAccelerate clang
> >
> > PS: IMO, Apply guys make "clang" sounds like GNU compiler.
> >
> > Hai
> >
> >
> > On Sat, Jan 21, 2017 at 12:53 AM, Karla Galdamez <kgalda.berkeley.edu>
> > wrote:
> >
> > > Hi everyone,
> > >
> > > Thank you for your previous response on installing AmberTools. I have
> > > followed the download on web link you mentioned below.
> > > http://ambermd.org/AmberTools16-get.html
> > > Then, I began to follow instructions on installment on pg.23 of Amber
> > 2016
> > > Reference manual under Sect. 2 Installation.
> > >
> > > I have executed the command (4):
> > > > ./configure --help
> > > > ./configure gnu
> > >
> > > And it looks like everything works well up to lgfortran. I am copying
> > > below the error listed. Would you have recommendations as to what to
> do
> > > next? - do you have a recommendation as to where to download lgfortran
> > > libraries for Mac OS? - Thank You!
> > >
> > > Testing the g++ compiler:
> > > g++ -fPIC -o testp testp.cpp
> > > OK
> > >
> > > Testing the gfortran compiler:
> > > gfortran -fPIC -O0 -o testp testp.f
> > > OK
> > >
> > > Testing mixed C/Fortran compilation:
> > > gcc -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -c -o
> > testp.c.o
> > > testp.c
> > > gfortran -fPIC -O0 -c -o testp.f.o testp.f
> > > gcc -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o testp
> > > testp.c.o testp.f.o -lgfortran -w
> > > ld: library not found for -lgfortran
> > > clang: error: linker command failed with exit code 1 (use -v to see
> > > invocation)
> > > ./configure2: line 2348: ./testp: No such file or directory
> > > Error: Unable to compile mixed C/Fortran code.
> > > Please check your compiler settings and configure flags.
> > > Configure failed due to the errors above!
> > >
> > > On Tue, Jan 17, 2017 at 10:47 PM, Nhai <nhai.qn.gmail.com> wrote:
> > >
> > > > Ah good point
> > > >
> > > > That link is meant to install required software to prepare for
> > installing
> > > > amber.
> > > >
> > > > You still need to download anbertools
> > > >
> > > > http://ambermd.org/AmberTools16-get.html
> > > >
> > > > Hai Nguyen
> > > >
> > > > > On Jan 18, 2017, at 1:24 AM, Karla Galdamez <kgalda.berkeley.edu>
> > > wrote:
> > > > >
> > > > > Hi,
> > > > >
> > > > > Thank you very much in advance for your help. I am trying to
> > download
> > > > > Amber on Mac OS from the link below.
> > > > > http://ambermd.org/amber_install.html
> > > > >
> > > > > I have followed the instructions including XCode, and typing the
> > > > suggested
> > > > > commands on the terminal line following instructions as suggested.
> > > > >
> > > > >
> > > > > Subsequently, I installed XQuartz, and gfortran. However, when I
> > write
> > > > > down the last command to install Amber: ./configure -macAccelerate
> > > clang,
> > > > > I obtain the response of : ' No such file or directory.
> > > > > I have included the command lines below.
> > > > >
> > > > > Thank you once more for your help!
> > > > > With kind regards,
> > > > > Karla
> > > > >
> > > > >
> > > > >> karlas-MacBook-Pro:~ karlagaldamez$ sudo xcodebuild -license
> > > > > Password:
> > > > > Apple Inc.
> > > > >
> > > > > Xcode and Apple SDKs Agreement
> > > > >
> > > > >
> > > > >> karlas-MacBook-Pro:~ karlagaldamez$ xcode-select --install
> > > > > xcode-select: error: command line tools are already installed, use
> > > > > "Software Update" to install updates
> > > > >> karlas-MacBook-Pro:~ karlagaldamez$ ./configure -macAccelerate
> clang
> > > > > -bash: ./configure: No such file or directory
> > > > >
> > > > >
> > > > >
> > > > > --
> > > > > Karla M. Galdamez, Ph.D
> > > > > Affiliate Researcher
> > > > > Physics Department
> > > > > University of California at Berkeley
> > > > > _______________________________________________
> > > > > AMBER mailing list
> > > > > AMBER.ambermd.org
> > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > AMBER.ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > >
> > >
> > >
> > > --
> > > Karla M. Galdamez, Ph.D
> > > Affiliate Researcher
> > > Physics Department
> > > University of California at Berkeley
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Karla M. Galdamez, Ph.D
> Affiliate Researcher
> Physics Department
> University of California at Berkeley
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Sat Jan 21 2017 - 00:00:02 PST
