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--- > VDWAALS = 1964.904 EEL = -18699.296 HBOND = 0. Hai > Thank you! > > > On Fri, Jan 20, 2017 at 11:43 PM, Hai Nguyen <nhai.qn.gmail.com> wrote: > > > 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 > > > > > _______________________________________________ > > 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/amberReceived on Sat Jan 21 2017 - 22:00:03 PST