[gmx-users] topology file

Michelle Aranha maranha at utk.edu
Wed Mar 19 19:22:52 CET 2014

I create a parallel job file with the following content
#$ -N prep66
#$ -pe openmpi* 12
#$ -cwd
#$ -q medium*

mpirun -np 12 /data/apps/gromacs/4.6.1/mpi/bin/editconf_mpi -f 66.pdb -o
cnt.gro -bt cubic -box 5 5 5 -c
mpirun -np 12 /data/apps/gromacs/4.6.1/mpi/bin/g_x2top_mpi -f cnt.gro -o
cnt.top -ff opls -name CNT
mpirun -np 12 /data/apps/gromacs/4.6.1/mpi/bin/genbox_mpi -cp cnt.gro -cs
spc216.gro -p cnt.top -o cntsol.gro
mpirun -np 12 /data/apps/gromacs/4.6.1/mpi/bin/genrestr_mpi -f cntsol.gro

During the process of running it creates several temp.top files which have
the correct output, however the final topology file I get has zero output. 
I would like to know if I am doing anything wrong.


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