[gmx-users] non-interactive script help

[Chandan Choudhury]

Thanks Terry.
It worked.

Chandan

--
Chandan kumar Choudhury
NCL, Pune
INDIA



On Fri, Jul 22, 2011 at 12:00 PM, Terry <terrencesun at gmail.com> wrote:
>
> 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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>
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