[gmx-users] non-interactive script help

[Terry]

You should issue a "q" command to save and quit. So "choice.txt" should look
like:

ri 1-20
...
...
ri 101-120
q


Cheers.

Terry


On Fri, Jul 22, 2011 at 1:53 PM, Chandan Choudhury <iitdckc at gmail.com>wrote:

> Hi gmx-users,
>
> I was trying to feed make_ndx with the non-interactive script, below
> is my command:
>
> The script called "choice.txt" contained:
>
>> ri 1-20
>
> ri 21-40
>
> ri 41-60
>
> ri 61-80
>
> ri 81-100
>
> ri 101-120
>
>
> Initially, I used the bash shell, then csh and tcsh, but in both the
> cases it failed to produce the index_1.ndx file
>
> $make_ndx -f md20-80.tpr -o index_1.ndx < choice.txt
>
> >
> Found 162 atoms with resind.+1 in range 1-20
>
>  5 r_1-20              :   162 atoms
>
> >
> Found 162 atoms with resind.+1 in range 21-40
>
>  6 r_21-40             :   162 atoms
>
> >
> Found 162 atoms with resind.+1 in range 41-60
>
>  7 r_41-60             :   162 atoms
>
> >
> Found 162 atoms with resind.+1 in range 61-80
>
>  8 r_61-80             :   162 atoms
>
> >
> Found 162 atoms with resind.+1 in range 81-100
>
>  9 r_81-100            :   162 atoms
>
> >
> Found 162 atoms with resind.+1 in range 101-120
>
>  10 r_101-120           :   162 atoms
>
>
> -------------------------------------------------------
> Program make_ndx, VERSION 4.5.4
> Source code file: make_ndx.c, line: 965
>
> Fatal error:
> Error reading user input
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
> Kindly help.
>
> Chandan
>
> --
> Chandan kumar Choudhury
> NCL, Pune
> INDIA
> --
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