[gmx-users] (no subject)

[حلیمه میرسالاری]

Dear all

l am using gromacs 4.5.5 version for simulation carbon nanotubes  with
charmm27 force feild ,there was no error grompp stage,but when l do
simulation of carbon nanotube in tip3p  water encountered with
 fatal error:

  [ file tip3p.itp, line 40]:
Atom index (1) in settles out of bounds (1-0).
This probably means that you have inserted topology section "settles"
in a part belonging to a different molecule than you intended to.
In that case move the "settles" section to the right molecule.

Please guide me

File:tip3p.itp

Thanks

Halimeh


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[ moleculetype ]
; molname      nrexcl
SOL		2

[ atoms ]
; id   at type	res nr	residu name	at name		cg nr	charge
#ifdef _FF_CHARMM
1       OWT3    1       SOL              OW             1       -0.834
2       HWT3    1       SOL             HW1             1        0.417
3       HWT3    1       SOL             HW2             1        0.417
#endif


#ifdef FLEXIBLE

#ifdef CHARMM_TIP3P
[ bonds ]
; i	j	funct	length	force.c.
1 	2	1	0.09572	376560.0 0.09572	376560.0
1	3	1	0.09572	376560.0 0.09572	376560.0

[ angles ]
; i	 j	k	funct	angle	force.c.
2 	 1	3	1	104.52	460.24	104.52	460.24	
#else
[ bonds ]
; i	j	funct	length	force.c.
1 	2	1	0.09572	502416.0 0.09572	502416.0
1 	3	1	0.09572	502416.0 0.09572	502416.0

[ angles ]
; i	 j	k	funct	angle	force.c.
2 	 1	3	1	104.52	628.02	104.52	628.02	
#endif


#else
[ settles ]
; i	  j	funct	length
1 	  1	0.09572	0.15139

[ exclusions ]
1 2 3
2 1 3
3 1 2
#endif