The GitHub cpptraj is a standalone install and should be done in its
own directory.
Anyway, since you have amber 14 the sander API there is probably not
compatible with the current iteration of cpptraj anyway. So disable
that as well:
./configure -amberlib -nobzlib -nosanderlib gnu
-Dan
On Wed, Mar 9, 2016 at 12:24 PM, Timothy Christopher Schutt
<tschutt.mymail.mines.edu> wrote:
> I don't think it installed - what I sent was the entirety of the prompt it
> gave me. I tried to type make install to test if it had configured and it
> said it couldn't without a config.h file so my guess is that the configure
> didn't finish without the sander API thing.
>
> Does this need to be performed in the ambertools bin folder? I've been
> trying to do it in a separate directory so as to preserve the working
> cpptraj just in case... My thought was that it could find all the necessary
> files even from a remote directory since amberhome is set but am I wrong in
> that perhaps?
>
> On Wed, Mar 9, 2016 at 11:07 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
>> In other words you should still see:
>>
>> CPPTRAJ configuration complete.
>>
>> On Wed, Mar 9, 2016 at 11:06 AM, Daniel Roe <daniel.r.roe.gmail.com>
>> wrote:
>> > Does configure actually fail at that point? It should just disable
>> > linking to the sander API.
>> >
>> > On Wed, Mar 9, 2016 at 11:02 AM, Timothy Christopher Schutt
>> > <tschutt.mymail.mines.edu> wrote:
>> >> ./configure -amberlib -nobzlib gnu
>> >>
>> >> Assuming 64 bit architecture.
>> >> Using BLAS/LAPACK/ARPACK/NetCDF libraries in
>> /home/mtux7/Software/amber14
>> >> Not using bzip2
>> >> SANDER API will be used if found.
>> >> Using gnu compilers
>> >> Installing cpptraj binary to
>> >> /home/mtux7/Software/Betacpptraj/cpptraj-master/bin
>> >>
>> >> Testing C compiler:
>> >> OK
>> >> Testing C++ compiler:
>> >> OK
>> >> Testing Fortran compiler:
>> >> OK
>> >> Checking ZLIB
>> >> OK
>> >> Checking NetCDF
>> >> OK
>> >> Checking LAPACK/BLAS
>> >> OK
>> >> Checking ARPACK
>> >> OK
>> >> Checking availability of the SANDER API from AmberTools
>> >> Using SANDER API from /home/mtux7/Software/amber14
>> >> ./testp: error while loading shared libraries: libsander.so: cannot open
>> >> shared object file: No such file or directory
>> >> Warning: Compilation with the SANDER API failed. Error follows:
>> >> --------------------
>> >> --------------------
>> >>
>> >>
>> >> On Wed, Mar 9, 2016 at 8:41 AM, Daniel Roe <daniel.r.roe.gmail.com>
>> wrote:
>> >>
>> >>> Hi,
>> >>>
>> >>> Admittedly the configure process could (and should) be made a bit
>> >>> easier. By default cpptraj assumes you want certain libraries for full
>> >>> functionality. In this case, bzlib is for reading bzip2-compressed
>> >>> files (i.e. those with a .bz2 extension). The Amber configure script
>> >>> automatically disables this when bzlib is not available. You can
>> >>> either install the bzip2 development headers/libraries via your
>> >>> package manager (I think it's usually called libbz2-dev or
>> >>> bzip2-devel) or you can disable bzip2 support with '-nobzlib'. Typing
>> >>> ./configure --full-help will give you a full list of configure
>> >>> options.
>> >>>
>> >>> So try ./configure -amberlib -nobzlib gnu and see if that works.
>> >>>
>> >>> -Dan
>> >>>
>> >>>
>> >>> On Tue, Mar 8, 2016 at 11:43 PM, Timothy Christopher Schutt
>> >>> <tschutt.mymail.mines.edu> wrote:
>> >>> > I apologize for my slow reply - I did try that at first but it came
>> up
>> >>> with
>> >>> > a BZLIB error. $AMBERHOME is set in the ~/.bashrc and the .bashrc is
>> >>> > sourced. This is what it gave me? I was lost so I went home and ate
>> some
>> >>> > dinner first.
>> >>> >
>> >>> > xxxxx$ ./configure -amberlib gnu
>> >>> >
>> >>> > Assuming 64 bit architecture.
>> >>> > Using BLAS/LAPACK/ARPACK/NetCDF libraries in
>> /home/mtux7/Software/amber14
>> >>> > SANDER API will be used if found.
>> >>> > Using gnu compilers
>> >>> > Installing cpptraj binary to
>> >>> > /home/mtux7/Software/Betacpptraj/cpptraj-master/bin
>> >>> >
>> >>> > Testing C compiler:
>> >>> > OK
>> >>> > Testing C++ compiler:
>> >>> > OK
>> >>> > Testing Fortran compiler:
>> >>> > OK
>> >>> > Checking BZLIB
>> >>> > ./configure: line 131: ./testp: No such file or directory
>> >>> > Error: Unable to compile using:
>> >>> > g++ -I/home/mtux7/Software/amber14/include -o testp
>> testp.cpp
>> >>> > -lbz2
>> >>> > Please check your compiler settings or configure flags. Error
>> follows:
>> >>> > --------------------
>> >>> > testp.cpp:2:19: fatal error: bzlib.h: No such file or directory
>> >>> > #include "bzlib.h"
>> >>> > ^
>> >>> > compilation terminated.
>> >>> > --------------------
>> >>> >
>> >>> > Thanks for all the help, all of you!!
>> >>> >
>> >>> > On Tue, Mar 8, 2016 at 9:43 PM, Daniel Roe <daniel.r.roe.gmail.com>
>> >>> wrote:
>> >>> >
>> >>> >> On Tue, Mar 8, 2016 at 6:05 PM, Timothy Christopher Schutt
>> >>> >> <tschutt.mymail.mines.edu> wrote:
>> >>> >> >
>> >>> >> > .Daniel: I'm having trouble compiling the beta cpptraj - I'm
>> pretty
>> >>> new
>> >>> >> to
>> >>> >> > linux and command line stuff so I'm sure that part is just me
>> being
>> >>> slow
>> >>> >> > but I'll figure it out here eventually.
>> >>> >>
>> >>> >> If you give some more specifics about what is going wrong I may be
>> >>> >> able to help. With the latest GitHub version of cpptraj with Amber
>> >>> >> already installed and AMBERHOME correctly set it should be as simple
>> >>> >> as:
>> >>> >>
>> >>> >> ./configure -amberlib gnu
>> >>> >>
>> >>> >> (Assuming of course you are using gnu compilers). Let me know if you
>> >>> >> need any more help,
>> >>> >>
>> >>> >> -Dan
>> >>> >>
>> >>> >> >
>> >>> >> > .Thomas: I just attempted the unwrap command and that totally
>> worked!!
>> >>> >> > Thanks! I'll be sure to include that from now on. I didn't realize
>> >>> that
>> >>> >> was
>> >>> >> > required at first because the diffusion command automatically
>> >>> accounted
>> >>> >> for
>> >>> >> > wrapping around in one dimension at a time.
>> >>> >> >
>> >>> >> > On Tue, Mar 8, 2016 at 5:34 PM, David A Case <
>> david.case.rutgers.edu>
>> >>> >> wrote:
>> >>> >> >
>> >>> >> >> On Tue, Mar 08, 2016, Timothy Christopher Schutt wrote:
>> >>> >> >> >
>> >>> >> >> > ...one molecule sitting on the box edge or corner happens to
>> cross
>> >>> the
>> >>> >> >> > boundary in two different dimensions during the same frame
>> change.
>> >>> In
>> >>> >> >> > this scenario the wrapping of the second periodic boundary is
>> not
>> >>> >> >> > accounted for and the MSD jumps up by n * L^2/N (L= simulation
>> box
>> >>> >> >> > length. n= number of molecules in the mask double wrapping that
>> >>> frame,
>> >>> >> >> > and N = the number of molecules in the mask).
>> >>> >> >>
>> >>> >> >> Are you trying to compute diffusion behavior from a trajectory
>> that
>> >>> was
>> >>> >> >> originally created with iwrap=1? Or that has been subject to the
>> >>> >> "image"
>> >>> >> >> or
>> >>> >> >> "autoimage" command in cpptraj? Just trying to pin down possible
>> >>> >> sources
>> >>> >> >> of
>> >>> >> >> problems.
>> >>> >> >>
>> >>> >> >> ....dac
>> >>> >> >>
>> >>> >> >>
>> >>> >> >> _______________________________________________
>> >>> >> >> 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
>> >>> >>
>> >>> >>
>> >>> >>
>> >>> >> --
>> >>> >> -------------------------
>> >>> >> Daniel R. Roe, PhD
>> >>> >> Department of Medicinal Chemistry
>> >>> >> University of Utah
>> >>> >> 30 South 2000 East, Room 307
>> >>> >> Salt Lake City, UT 84112-5820
>> >>> >> http://home.chpc.utah.edu/~cheatham/
>> >>> >> (801) 587-9652
>> >>> >> (801) 585-6208 (Fax)
>> >>> >>
>> >>> >> _______________________________________________
>> >>> >> 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
>> >>>
>> >>>
>> >>>
>> >>> --
>> >>> -------------------------
>> >>> Daniel R. Roe, PhD
>> >>> Department of Medicinal Chemistry
>> >>> University of Utah
>> >>> 30 South 2000 East, Room 307
>> >>> Salt Lake City, UT 84112-5820
>> >>> http://home.chpc.utah.edu/~cheatham/
>> >>> (801) 587-9652
>> >>> (801) 585-6208 (Fax)
>> >>>
>> >>> _______________________________________________
>> >>> 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
>> >
>> >
>> >
>> > --
>> > -------------------------
>> > Daniel R. Roe, PhD
>> > Department of Medicinal Chemistry
>> > University of Utah
>> > 30 South 2000 East, Room 307
>> > Salt Lake City, UT 84112-5820
>> > http://home.chpc.utah.edu/~cheatham/
>> > (801) 587-9652
>> > (801) 585-6208 (Fax)
>>
>>
>>
>> --
>> -------------------------
>> Daniel R. Roe, PhD
>> Department of Medicinal Chemistry
>> University of Utah
>> 30 South 2000 East, Room 307
>> Salt Lake City, UT 84112-5820
>> http://home.chpc.utah.edu/~cheatham/
>> (801) 587-9652
>> (801) 585-6208 (Fax)
>>
>> _______________________________________________
>> 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
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
_______________________________________________
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http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Mar 09 2016 - 12:00:02 PST
