> testp.cpp:2:19: fatal error: bzlib.h: No such file or directory
You could try 'find / -name bzlib.h' and figure out how to screen the
error msgs to see if you have it. Likely not.
What OS are you on? Try to figure out whether you can install bzlib via
apt_get, brew, or whatever similar works for your system.
Bill
On 3/8/16 10:43 PM, Timothy Christopher Schutt 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
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>>>> 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
>>
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Received on Wed Mar 09 2016 - 00:30:04 PST
