[gmx-users] Creating .ndx for TIP5Pwater

[Mark Abraham]

JMandumpal wrote:
> Dear David,
> 
> 
> I didn't get the desired box length when I tried to use editconf command 
> ( I took the tip5p box from gromacs/tutor directory) . Then, I tried 
> editconf command to generate .gro file using myown water box. It worked!!

I'll bet my car that you did something wrong the first time, and not the 
second time :-)

> Still, there is a problem. How can I create .ndx file?- I tried 
> make_ndx -n tip5p_W.pdb, but it resulted in a message: input/output error.

Curiously enough, one of your inputs or outputs is wrong. :-) Have a 
read of man make_ndx and you should see your problem.

> Could you suggest an alternative way for builing up ndx files?

http://wiki.gromacs.org/index.php/Index_File

Mark