[gmx-users] Creating .ndx for TIP5Pwater
Mark Abraham
Mark.Abraham at anu.edu.au
Tue Nov 20 09:03:13 CET 2007
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
More information about the gromacs.org_gmx-users
mailing list