# Re: [AMBER] Installing Amber

From: Karla Galdamez <kgalda.berkeley.edu>
Date: Tue, 24 Jan 2017 22:29:22 -0800

Hello,

Would anyone be able to point me as to where to find Linearized
Semiclassical Initial Value Representation (LSC-IVR) code? - I was
informed that it would be in sander.

Thank you!
Karla

On Sat, Jan 21, 2017 at 9:55 PM, Hai Nguyen <nhai.qn.gmail.com> wrote:

> On Sun, Jan 22, 2017 at 12:44 AM, Karla Galdamez <kgalda.berkeley.edu>
> wrote:
>
> > Hi Hai, Bill and everyone,
> >
> > Thank you for your input! The installation has gone well, now I am
> running
> > 'make test' command. The result is that most file comparison passed and
> 5
> > failed (copied below).
> >
> > 1859 file comparisons passed
> > 5 file comparisons failed
> > 0 tests experienced errors
> >
> > I have taken a look under \logs\test_at_serial directory to view the 5
> > failed file comparison. I wonder as to how to go about fixing them
> > (attached), particularly the last one:
> >
>
>
>
> > possible FAILURE: check MG_QM_water_MM.out.dif
> >
> >
> this is rounding issue. You can ignore it.
>
> e.g:
>
> < VDWAALS = 1964.904 EEL = -18699.295 HBOND = 0.
> ---
> > 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
> > > > 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
> > > > 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
> > > > > > 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
> > > > > > > > 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/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
```
Received on Tue Jan 24 2017 - 22:30:02 PST
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