Hi there,
When I try:
make clean
/bin/rm *.o _*.f make_crd_hg molsurf
/bin/rm: cannot remove `make_crd_hg': No such file or directory
/bin/rm: cannot remove `molsurf': No such file or directory
make: [clean] Error 1 (ignored)
make install
cpp -traditional -I/usr/local/include -P -xassembler-with-cpp
-Dsecond=ambsecond -DBINTRAJ -DMPI make_crd_hg.f > _make_crd_hg.f
/usr/local/bin/mpif90 -c -O0 -fno-range-check -fno-second-underscore -o
make_crd_hg.o _make_crd_hg.f
/usr/local/bin/mpif90 -o make_crd_hg make_crd_hg.o ../lib/amopen.o
../lib/mexit.o
/usr/bin/ld: skipping incompatible /usr/local/lib/libgcc_s.so when searching
for -lgcc_s
/usr/bin/ld: skipping incompatible /usr/local/lib/libgcc_s.so when searching
for -lgcc_s
/usr/bin/ld: warning: libgfortran.so.1, needed by
/usr/local/lib/libmpi_f90.so, may conflict with libgfortran.so.3
/usr/bin/ld: warning: libgfortran.so.1, needed by
/usr/local/lib/libmpi_f90.so, may conflict with libgfortran.so.3
gcc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -O2 -m64 -DBINTRAJ
-I../netcdf/include -o molsurf.o molsurf.c
gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -O2 -m64 -o molsurf
molsurf.o -lm
mv make_crd_hg molsurf ../../exe
cp mm_pbsa.pl mm_pbsa_statistics.pl ../../exe
and then just to catch errors:
/array2/programs/amber10/exe/mm_pbsa.pl mmpbsa.in > LOG
"$HTMLPATH" is not exported by the mm_pbsa_global module
Can't continue after import errors at /array2/programs/amber10/src/mm_pbsa/
mm_pbsa_createinput.pm line 21
BEGIN failed--compilation aborted at /array2/programs/amber10/src/mm_pbsa/
mm_pbsa_createinput.pm line 23.
Compilation failed in require at /array2/programs/amber10/exe/mm_pbsa.plline 26.
BEGIN failed--compilation aborted at
/array2/programs/amber10/exe/mm_pbsa.plline 26.
Any ideas?
On 21 September 2010 11:53, Bill Miller III <brmilleriii.gmail.com> wrote:
> You should be able to
>
> cd $AMBERHOME/src/mm_pbsa
> make clean
> make install
>
> That should do it.
>
> Good luck!
>
> -Bill
>
> On Tue, Sep 21, 2010 at 6:07 AM, Oliver Grant <olivercgrant.gmail.com
> >wrote:
>
> > Hi there,
> >
> > I have a fillratio error when running mm_pbsa.pl in Amber 10. It has
> come
> > up
> > on the mailing list a few times.
> >
> > I've followed the instructions in the threads and changed
> > mm_pbsa_createinput.pm to contain a line fillratio = 4
> >
> > Now I have to recomplie the perl script but I'm not sure how to do this.
> > I've checked the ambertools manual and threads but can't find
> instructions.
> >
> > Would someone be able to help me out?
> >
> > Thanks in advance for your help,
> >
> > Oliver
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Bill Miller III
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-6715
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue Sep 21 2010 - 05:00:05 PDT
