Dear David,
Now, the AMBERHOME variable setting is ok.
After using make install,
--------------------------------------------------------------------------------
[root.ibbs ptraj]# make install
cd pdb && make
make[1]: Entering directory
`/export/apps/amber/amber14/AmberTools/src/ptraj/pdb'
ar rv libpdb.a pdbrun.o pdb_read.o pdb_sprntf.o pdb_sscanf.o pdb_write.o
ms.o
ar: creating libpdb.a
a - pdbrun.o
a - pdb_read.o
a - pdb_sprntf.o
a - pdb_sscanf.o
a - pdb_write.o
a - ms.o
ranlib libpdb.a
mv libpdb.a /export/apps/amber/amber14/lib
make[1]: Leaving directory
`/export/apps/amber/amber14/AmberTools/src/ptraj/pdb'
cd ../arpack && make
make[1]: Entering directory
`/export/apps/amber/amber14/AmberTools/src/arpack'
make[1]: Nothing to be done for `install'.
make[1]: Leaving directory
`/export/apps/amber/amber14/AmberTools/src/arpack'
mpicc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ
-DHASBZ2 -DMPI -I/export/apps/amber/amber14/include -o main.o main.c
In file included from ptraj.h:80,
from main.c:114:
netcdf_ptraj.h:4:39: error: ../../include/pnetcdf.h: No such file or
directory
In file included from ptraj.h:80,
from main.c:114:
netcdf_ptraj.h:18: error: expected declaration specifiers or '...' before
'nc_type'
make: *** [main.o] Error 1
--------------------------------------------------------------------------------
This time, I encountered with only one error (Error 1).
On Wed, Oct 12, 2016 at 4:29 AM, David A Case <david.case.rutgers.edu>
wrote:
> On Tue, Oct 11, 2016, shahab shariati wrote:
>
> > [root.ibbs ptraj]# make install
> > cd pdb && make
> > make[1]: Entering directory `/share/apps/2_amber/amber14/
> AmberTools/src/ptraj/pdb'
>
> Here you are in the tree /share/apps/2_amer/amber14....
>
> > mv: cannot move `libpdb.a' to `/export/apps/amber/amber14/lib': No such
> > file or directory
>
> Here, it looks like your AMBERHOME variable is set to
> /export/apps/amber/amber14.
>
> I suspect that, as the message says, you don't have an
> /export/apps/amber/amber14/lib directory, and that you AMBERHOME variable
> is
> probably set incorrectly.
>
> Having said that, the advice to move to acpype sounds like a much better
> solution.
>
> ....dac
>
> [Aside: don't install Amber as root! Take the time to learn how to avoid
> doing this.]
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed Oct 12 2016 - 05:30:04 PDT
