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

[Joern Lenz]

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