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
>
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--
-------------------------
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
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Received on Tue Sep 29 2015 - 16:00:03 PDT
