Dear Amber users
I am trying to run cpptraj to extract particular frames from the trajectory
file. It works fine when i use these command one by one after opening
CPPTRAJ
(extract-frames.cpptraj)
parm wet.complex.prmtop
trajin md1.mdcrd
strip :WAT,Na+ outprefix stripped
trajout out_frame.pdb pdb multi nobox onlyframes 19,1
But when I try to run it through script its does not work
my .sh file is this
#!/bin/sh
#$ -S /bin/bash
#$ -V
#$ -cwd
#$ -j y
#$ -r y
#$ -N md
#$ -o LOGFILES_energy_O
#$ -e LOGFILES_energy_E
#### #$ -pe amber 42
#$ -pe amber 1
cpptraj -p wet.complex.prmtop -i extract-frames.cpptraj
Kindly guide
thanks
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Received on Wed Oct 06 2021 - 09:30:02 PDT
