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

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Oct 30 08:27:32 CET 2008

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:

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.



---------- 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>

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

Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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