hi,
I am using amber14 and Ambertool 14 when i type MMPBSA.py --clean or MMPBSA.py --version it is generating error zsh: command not found: MMPBSA.py.
and when i run the command ./MMPBSA.py it is again showing the same Error
Error: ptraj is needed for MMPBSA.
ayesha.ayesha-Inspiron-3521[amber14] export AMBERHOME=/home/ayesha/Desktop/amber14
ayesha.ayesha-Inspiron-3521[amber14] export PATH="$/home/ayesha/Desktop/amber14/bin:$PATH"
ayesha.ayesha-Inspiron-3521[amber14] cd bin
ayesha.ayesha-Inspiron-3521[bin] MMPBSA.py --clean
zsh: command not found: MMPBSA.py
ayesha.ayesha-Inspiron-3521[bin] MMPBSA.py --version
zsh: command not found: MMPBSA.py
ayesha.ayesha-Inspiron-3521[bin] ./MMPBSA.py
Error: ptraj is needed for MMPBSA
NOTE: All files have been retained for debugging purposes. Type MMPBSA.py --clean to erase these files.
> Date: Tue, 29 Sep 2015 16:52:16 -0600
> From: daniel.r.roe.gmail.com
> To: amber.ambermd.org
> Subject: Re: [AMBER] Error: ptraj is needed for MMPBSA
>
> Hi,
>
> This is a strange error indeed - mmpbsa.py currently uses cpptraj
> under the hood for trajectory processing. I don't think mmpbsa.py has
> used ptraj since version 12 (if I'm remembering correctly). What are
> the results of the following commands:
>
> which MMPBSA.py
> MMPBSA.py --version
>
> -Dan
>
> On Tue, Sep 29, 2015 at 4:07 PM, Ayesha Kanwal
> <ayesha_comsian.hotmail.com> wrote:
> > Hi,
> > i installed ptraj in AmberTools/src/ptraj but it generate error that ptraj is needed for MMPBSA
> > the commands are following that i used for installation of ptraj:
> >
> > ayesha.ayesha-Inspiron-3521[amber14] cd $AMBERHOME/AmberTools/src/ptraj
> >
> > ayesha.ayesha-Inspiron-3521[ptraj] make install [11:13PM]
> >
> > cd pdb && make
> > make[1]: Entering directory `/home/ayesha/Desktop/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 /home/ayesha/Desktop/amber14/lib
> > make[1]: Leaving directory `/home/ayesha/Desktop/amber14/AmberTools/src/ptraj/pdb'
> > cd ../arpack && make
> > make[1]: Entering directory `/home/ayesha/Desktop/amber14/AmberTools/src/arpack'
> > make[1]: Nothing to be done for `install'.
> > make[1]: Leaving directory `/home/ayesha/Desktop/amber14/AmberTools/src/arpack'
> > gcc -DSYSV -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 \
> > -o rdparm main.o rdparm.o dispatch.o help.o utility.o second.o io.o trajectory.o netcdf_ptraj.o parallel_ptraj.o evec.o torsion.o mask.o rms.o display.o interface.o energy.o experimental.o ptraj.o actions.o analyze.o thermo.o pubfft.o cluster.o clusterLib.o -L/home/ayesha/Desktop/amber14/lib -lpdb -larpack -llapack -lblas -lgfortran -w /home/ayesha/Desktop/amber14/lib/libnetcdf.a -lm
> > cd ../lapack && make install
> > make[1]: Entering directory `/home/ayesha/Desktop/amber14/AmberTools/src/lapack'
> > make[1]: Nothing to be done for `install'.
> > make[1]: Leaving directory `/home/ayesha/Desktop/amber14/AmberTools/src/lapack'
> > cd ../blas && make install
> > make[1]: Entering directory `/home/ayesha/Desktop/amber14/AmberTools/src/blas'
> > make[1]: Nothing to be done for `install'.
> > make[1]: Leaving directory `/home/ayesha/Desktop/amber14/AmberTools/src/blas'
> > gcc -DSYSV -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 \
> >
> > -o ptraj main.o rdparm.o dispatch.o help.o utility.o second.o io.o trajectory.o netcdf_ptraj.o parallel_ptraj.o evec.o torsion.o mask.o rms.o display.o interface.o energy.o experimental.o ptraj.o actions.o analyze.o thermo.o pubfft.o cluster.o clusterLib.o -L/home/ayesha/Desktop/amber14/lib -lpdb -larpack -llapack -lblas -lgfortran -w /home/ayesha/Desktop/amber14/lib/libnetcdf.a -lm
> > /bin/mv rdparm ptraj /home/ayesha/Desktop/amber14/bin
> >
> >
> > But after that when i put the following command then why it generate this error i could not understand this please guide me my AMBERHOME set is :
> >
> > export AMBERHOME=/home/ayesha/Desktop/amber14
> >
> > ayesha.ayesha-Inspiron-3521[amber14] $AMBERHOME/bin/MMPBSA.py -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat -sp ras-raf_solvated.prmtop -cp ras-raf.prmtop -rp ras.prmtop -lp raf.prmtop -y ras-raf_top_mdcrd.mdcrd
> >
> > Am i missed something ? or do something wrong please guide me
> >
> > Error: ptraj is needed for MMPBSA
> > NOTE: All files have been retained for debugging purposes. Type MMPBSA.py --clean to erase these files.
> >
> > In advance thank you
> > with regards
> > Ayesha Kanwal
> >
> > _______________________________________________
> > 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)
>
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Received on Wed Sep 30 2015 - 08:00:03 PDT
