Chih-Ying Lin wrote:
Hi
I have the following error when I Add water spc216.gro.
[ file "/usr/local/gromacs/share/gromacs/top/spc.itp", line 41 ]:
Atom index (1) in settles out of bounds (1-0)
From the Archieve,
http://www.gromacs.org/pipermail/gmx-users/2007-March/026171.html
Quote
=> "spc.itp includes a [ molecule ] section, all of
which must occur before the [ molecules ] section (and you don't want to
start a new [ molecule ] before the old one has finished, either!)"
1. "spc.itp includes a [ molecule ] section, all of
which must occur before the [ molecules ] section"
=> did it as the chapter 5, page 103 of tutorial
=> the error is still there.
2. "you don't want to start a new [ molecule ] before the old one has
finished, either! "
=> how to complete this part?
We can't tell what you've done wrong unless you show us what you've done.
The page 103 of tutorial,
; The force field files to be included
#include "ffgmx.itp"
;Include urea topology
#include "spc.itp"
[system]
Urea in water
[molecules]
; molecule name number
Urea 1
SOL 1000
I'm not sure if the above is your attempt or the tutorial material, but
it won't work, because the "Urea" molecule is never defined.
Mark
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