[gmx-users] ERROR IN BASH SCRIPTING

Mark Abraham mark.j.abraham at gmail.com
Tue Feb 28 10:01:59 CET 2017


Hi,

Looks like you edited on Windows last. Use dos2unix now, or a proper text
editor next time ;-)

Mark

On Tue, 28 Feb 2017 08:14 Subashini .K <subashinik at hotmail.com> wrote:

> Hi gromacs users,
>
>
> I use the following run.sh in the working directory of simulations
>
>
> #!/bin/bash
> set -e
>
> for ((i=0;i<27;i++)); do
>
>     x=$(echo "0.05*$(($i+1))" | bc);
>
>     sed 's/WINDOW/'$x'/g' mdp/min.mdp > grompp.mdp
>     gmx grompp -o min.$i -pp min.$i -po min.$i -n index.ndx
>     gmx mdrun -deffnm min.$i -pf pullf-min.$i -px pullx-min.$i
>
>     sed 's/WINDOW/'$x'/g' mdp/min2.mdp > grompp.mdp
>     gmx grompp -o min2.$i -c min.$i -t min.$i -pp min2.$i -po min2.$i
> -maxwarn 1 -n index.ndx
>     gmx mdrun -deffnm min2.$i -pf pullf-min2.$i -px pullx-min2.$i
>
>     sed 's/WINDOW/'$x'/g' mdp/eql.mdp > grompp.mdp
>     gmx grompp -o eql.$i -c min2.$i -t min2.$i -pp eql.$i -po eql.$i -n
> index.ndx
>     gmx mdrun -deffnm eql.$i -pf pullf-eql.$i -px pullx-eql.$i
>
>     sed 's/WINDOW/'$x'/g' mdp/eql2.mdp > grompp.mdp
>     gmx grompp -o eql2.$i -c eql.$i -t eql.$i -pp eql2.$i -po eql2.$i -n
> index.ndx
>     gmx mdrun -deffnm eql2.$i -pf pullf-eql2.$i -px pullx-eql2.$i
>
>     sed 's/WINDOW/'$x'/g' mdp/prd.mdp > grompp.mdp
>     gmx grompp -o prd.$i -c eql2.$i -t eql2.$i -pp prd.$i -po prd.$i -n
> index.ndx
>     gmx mdrun -deffnm prd.$i -pf pullf-prd.$i -px pullx-prd.$i
>
> done
>
> However, I get the following error
>
>
>  ./run.sh
> : invalid option: set: -
> set: usage: set [-abefhkmnptuvxBCHP] [-o option-name] [--] [arg ...]
> ./run.sh: line 3: $'\r': command not found
> ./run.sh: line 4: syntax error near unexpected token `$'do\r''
> '/run.sh: line 4: `for ((i=0;i<27;i++)); do
>
>
> How to fix it?
>
>
> Thanks,
>
> Subashini.K
>
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