[gmx-users] Problem with position restraints

[Ben Tehan]

To fellow gromacs users,
	I am having some unexpected problems when trying to setup initial
dynamics with restraints, has anyone seen this before?

>grompp -f pr.mdp -c post_min.gro -p 1a1v.top -o pr.tpr

Warning: as of GMX v 2.0 unit of compressibility is truly 1/bar
checking input for internal consistency...
calling /lib/cpp...
processing topology...
Generated 135 of the 1081 non-bonded parameter combinations
Cleaning up temporary file gromppdOxKKF
Fatal error: [ file "posre.itp", line 9 ]:
             Atom index (4) in position_restraints out of bounds (1-1)




>>posre.itp
; In this topology include file, you will find position restraint
; entries for all the heavy atoms in your original pdb file.
; This means that all the protons which were added by pdb2gmx are
; not restrained.

[ position_restraints ]
; atom  type      fx      fy      fz
     1     1  1000  1000  1000
     4     1  1000  1000  1000
     5     1  1000  1000  1000
etc...

>>post_min.gro
Hepatitis B
53648
    1PRO      N    1   4.430   5.708   1.998
    1PRO     H1    2   4.468   5.630   2.049
    1PRO     H2    3   4.449   5.694   1.900
    1PRO     CA    4   4.286   5.719   2.026
    1PRO     CB    5   4.266   5.854   2.095
    1PRO     CG    6   4.404   5.885   2.150
    1PRO     CD    7   4.499   5.829   2.045
    1PRO      C    8   4.204   5.725   1.896
etc...


I appreciate any insights that anyone is able to give me with this
problem.
The posre.itp file is the one generated when first running pdb2gmx and I
can't see anything wrong with it. 
Thanks in advance,
Ben.