Dear David,
Thanks for your answer.
Based on your suggestion, I did following:
cd to $AMBERHOME/AmberTools/src/ptraj and type "make install"
[root.ibbs ptraj]# make install
cd pdb && make
make[1]: Entering directory `/share/apps/2_amber/amber14/
AmberTools/src/ptraj/pdb'
mpicc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2
-DMPI -c -o pdbrun.o pdbrun.c
mpicc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2
-DMPI -c -o pdb_read.o pdb_read.c
mpicc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2
-DMPI -c -o pdb_sprntf.o pdb_sprntf.c
mpicc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2
-DMPI -c -o pdb_sscanf.o pdb_sscanf.c
mpicc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2
-DMPI -c -o pdb_write.o pdb_write.c
mpicc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2
-DMPI -c -o ms.o ms.c
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
mv: cannot move `libpdb.a' to `/export/apps/amber/amber14/lib': No such
file or directory
make[1]: *** [libpdb.a] Error 1
make[1]: Leaving directory `/share/apps/2_amber/amber14/
AmberTools/src/ptraj/pdb'
make: *** [libs] Error 2
On Tue, Oct 11, 2016 at 9:22 PM, David A Case <david.case.rutgers.edu>
wrote:
> On Tue, Oct 11, 2016, shahab shariati wrote:
> >
> > I want to convert prmtop and inpcrd file (created using antechamber) to
> > gromacs files using amb2gmx.pl.
> >
> > When I use command:./amb2gmx.pl --prmtop lig.prmtop -crd lig.inpcrd
> > -outname lig, I encontered with:
>
> > sh: rdparm: command not found
>
> The amb2gmx.pl script (which is not a part of Amber) expects to find a
> program
> called "rdparm". The latter used to be a part of Amber, but is no longer
> distributed.
>
> The best thing to do is to contact the authors of this script (Gromacs
> team?)
> and see if they have an updated version.
>
> Less good, but might work: you can cd to $AMBERHOME/AmberTools/src/ptraj
> and
> type "make install"; this will put rdparm into $AMBERHOME/bin. It that is
> in
> your PATH, then the amb2gmx script might work.
>
> ....dac
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue Oct 11 2016 - 12:00:02 PDT
