[gmx-users] The question from the tutorial: Add water spc216.gro

[Mark Abraham]

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