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

[Chih-Ying Lin]

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?

Thank you
Lin


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







Hi Lin,

This is also gromacs related, rather than tutorial related. You
followed the tutorial and now went off to try the procedures on your
own system.

As for the question, searching the user list with "settles" and
"bounds" gives me the following:
http://www.gromacs.org/pipermail/gmx-users/2007-March/026169.html

To me that's a rater "exact answer in the Archives of Gromacs".
Apparently the spc.itp is included in the wrong place in your topology
file. Time to read chapter 5 of the manual and get acquainted with the
topology file format.

Cheers,

Tsjerk

---------- Forwarded message ----------
From: Chih-Ying Lin <chihying2008 at gmail.com>
Date: Thu, Oct 30, 2008 at 7:35 AM
Subject: The question from the tutorial: Add water spc216.gro
To: Tsjerk Wassenaar <tsjerkw at gmail.com>


Hi
I have a molecule, which is not a protein.
Then, I made a .top and a .gro file manually.
And, I will like to see it in the water.



I followed all the procedures I learned from the tutorials.
The easiest way for me is to use all the commands and all of the .mdp
files from the tutorials.


But, I met the problem when I tried to add water into the system
genbox -cp 1LW9-PBC.gro -cs spc216.gro -p 1LW9.top -o 1LW9-water.gro
It showed :
[ file "/usr/local/gromacs/share/gromacs/top/spc.itp", line 41 ]:
 Atom index (1) in settles out of bounds (1-0)


I could not find the exact answer in the Archives of Gromacs and it
seems that everything is reasonable for me.

Would you please instruct me what is the possible error I made?

Thank you very much
Lin