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
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