<div><br></div>You should issue a "q" command to save and quit. So "choice.txt" should look like:<div><br></div><div>ri 1-20</div><div>...</div><div>...</div><div>ri 101-120</div><div>q</div><div><br></div>
<div><br></div><div>Cheers.</div><div><br></div><div>Terry</div><div><br><div><div><br><div class="gmail_quote">On Fri, Jul 22, 2011 at 1:53 PM, Chandan Choudhury <span dir="ltr"><<a href="mailto:iitdckc@gmail.com">iitdckc@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">Hi gmx-users,<br>
<br>
I was trying to feed make_ndx with the non-interactive script, below<br>
is my command:<br>
<br>
The script called "choice.txt" contained:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">ri 1-20</blockquote><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
ri 21-40</blockquote><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">ri 41-60</blockquote><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
ri 61-80</blockquote><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">ri 81-100</blockquote><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
ri 101-120</blockquote>
<br>
Initially, I used the bash shell, then csh and tcsh, but in both the<br>
cases it failed to produce the index_1.ndx file<br>
<br>
$make_ndx -f md20-80.tpr -o index_1.ndx < choice.txt<br>
<br>
><br>
Found 162 atoms with resind.+1 in range 1-20<br>
<br>
5 r_1-20 : 162 atoms<br>
<br>
><br>
Found 162 atoms with resind.+1 in range 21-40<br>
<br>
6 r_21-40 : 162 atoms<br>
<br>
><br>
Found 162 atoms with resind.+1 in range 41-60<br>
<br>
7 r_41-60 : 162 atoms<br>
<br>
><br>
Found 162 atoms with resind.+1 in range 61-80<br>
<br>
8 r_61-80 : 162 atoms<br>
<br>
><br>
Found 162 atoms with resind.+1 in range 81-100<br>
<br>
9 r_81-100 : 162 atoms<br>
<br>
><br>
Found 162 atoms with resind.+1 in range 101-120<br>
<br>
10 r_101-120 : 162 atoms<br>
<br>
<br>
-------------------------------------------------------<br>
Program make_ndx, VERSION 4.5.4<br>
Source code file: make_ndx.c, line: 965<br>
<br>
Fatal error:<br>
Error reading user input<br>
For more information and tips for troubleshooting, please check the GROMACS<br>
website at <a href="http://www.gromacs.org/Documentation/Errors" target="_blank">http://www.gromacs.org/Documentation/Errors</a><br>
<br>
Kindly help.<br>
<br>
Chandan<br>
<br>
--<br>
Chandan kumar Choudhury<br>
NCL, Pune<br>
INDIA<br>
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