[gmx-users] a problem with grompp

[Banafsheh Mehrazma]

Dear all;
I am trying to constrain a double stranded DNA, I have made an index
file and a posre.itp file, and then when I wanted to run grompp
command I have encountered this:
...........................................
Program grompp, VERSION 4.5.3
Source code file: toppush.c, line: 1526

Fatal error:
[ file posre_DNA.itp, line 318 ]:
Atom index (314) in position_restraints out of bounds (1-313).
This probably means that you have inserted topology section
"position_restraints"
in a part belonging to a different molecule than you intended to.
In that case move the "position_restraints" section to the right molecule.
...........................................................................

and the following lines are some parts of my .mdp file;
......................................................................................
title		= DNA NVT equilibration
define		= -DPOSRES_DNA	; position restrain the DNA
; Run parameters
integrator	= md		; leap-frog integrator
nsteps		= 75000		; 2 * 75000 = 150 ps

; Temperature coupling is on
tcoupl		= V-rescale	; modified Berendsen thermostat
tc-grps		= DNA   Water_and_ions
tau_t		= 0.1 	0.1		; time constant, in ps
ref_t		= 310 	310		
.........................................................................................
 and my topl.top is the following lines;



; Include forcefield parameters
#include "amber99.ff/forcefield.itp"

; Include chain topologies
#include "topol_DNA_chain_A.itp"
#include "topol_DNA_chain_B.itp"

#ifdef POSRES_DNA
#include "posre_DNA.itp"
#endif

; Include water topology
#include "amber99.ff/tip3p.itp"

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct       fcx        fcy        fcz
   1    1       1000       1000       1000
#endif

; Include topology for ions
#include "amber99.ff/ions.itp"

[ system ]
; Name
Protein in water

[ molecules ]
; Compound        #mols
DNA_chain_A         1
DNA_chain_B         1
SOL         5580
NA          18

..............................................................................................


what do you suggest that I do to make it work?
Thank you
B.Mehrazma