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
Received on Tue Mar 08 2016 - 23:00:04 PST
