[gmx-users] Fwd: Atom index (1) in settles out of bounds (1-0)

[Joern Lenz]

Sorry,
I digged through the post-list of old user-questions and found the same 
problem occuring.
the answer to the question was written by David v.d.Spoel and was:
"the position in the top file where the spc.itp was included is wrong".

In my top file this include statement is at the end of the script.
Where should it be ?
Thanks 
Joern

----------  Forwarded Message  ----------

Subject: Atom index (1) in settles out of bounds (1-0)
Date: Wednesday 07 March 2007 10:53
From: Joern Lenz <JLenz at zbh.uni-hamburg.de>
To: gmx-users at gromacs.org

Dear users,
I have a question regarding a simulation (using the amber ports) of DNA
covalently bound to a protein.
First of all I made an entry in the specbond.dat and the bond was correctly
build between the a P of the DNA and a Tyr of the protein.
After that I started grompp and got the following error:

Program grompp, VERSION 3.3.1
Source code file: toppush.c, line: 1108

Fatal error:
[ file ".../bin/x86_64-unknown-linux-gnu/share/gromacs/top/spc.itp", line
41 ]:
             Atom index (1) in settles out of bounds (1-0)

the content of the spc.itp file in line 41 is (marked with "==>>":

#ifdef FLEXIBLE
[ bonds ]
; i	j	funct	length	force.c.
1	2	1	0.1	345000	0.1     345000
1	3	1	0.1	345000	0.1     345000

[ angles ]
; i	j	k	funct	angle	force.c.
2	1	3	1	109.47	383	109.47	383
#else
[ settles ]
        ; OW	funct	doh	dhh
==>> 1 	1	0.1	0.16330

Can anyone tell me how to avoid this error and go on with simulations ?
Many thanks in advance
Joern

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