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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Received on Tue Sep 29 2015 - 15:30:03 PDT
