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
>> >>
>> >>
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>> >>
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>>
>>
>> --
>> -------------------------
>> 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
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
> _______________________________________________
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> 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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Received on Wed Mar 09 2016 - 08:00:03 PST
