[gmx-developers] automatization of make_ndx

leonardo seplveda leosfere at hotmail.com
Fri May 21 00:21:50 CEST 2004

Hello , I was trying to automatize the input of make_ndx to process a lot of 
structures. I maked a short perl script to create a group for each residue, 
which is

system("make_ndx -f p.gro -o index.ndx &");

for ($i=1;$i<=number of residues;$i++){
        system("r $i\n &");

system("q\n &");

the firt system call it is ok, but the second and the last do not print 
anything;it only  change of line, making an infinite loop. A friend tried to 
do the same in bash, and it do not work either. I dont have problems to 
print an entry with  system("r $i\n &"); to select the FF number in pdb2mx, 
I really do not know what is happening.


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