I'm still working on updating ACPYPE for new GAFF2 but it still works fine
for anything else. For now, you can follow
https://code.google.com/archive/p/acpype/ to get it.
ACPYPE is far better than amb2gmx.pl and won't even need AmberTools if you
just want to covert Amber topology to GMX.
Alan
On 11 October 2016 at 19:50, shahab shariati <shahab.shariati.gmail.com>
wrote:
> 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
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Alan Wilter SOUSA da SILVA, DSc
Senior Bioinformatician, UniProt
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom
Tel: +44 (0)1223 494588
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Received on Tue Oct 11 2016 - 15:00:03 PDT
