[gmx-users] Strange solvation error

[Raj Badhan]

Dear users,
I have a strange error for you. Whilst solvating my dimer with 
ligand, I get the following error:

Fatal error: realloc for nl->iinr (40509752 bytes, file 
C:\source\gromacs-3.1.
src\mdlib\ns.c, line 97, nl->iinr=0x0x       0): No such file or 
directory

which appears at the end of the following usual messages from 
genbox. 
Any ideas?
Many thanks



Reading solute configuration
?
Containing 7252 atoms in 466 residues
Initialising van der waals distances...
Opening library file C:\Gromacs\share\top\vdwradii.dat
Opening library file C:\Gromacs\share\top\aminoacids.dat
Van der Waals radius of atom 63ATP 1  O3 set to 0.105
Van der Waals radius of atom 63ATP 1  PG set to 0.105
Van der Waals radius of atom 63ATP 1  O2 set to 0.105
Van der Waals radius of atom 63ATP 1  O1 set to 0.105
Van der Waals radius of atom 63ATP 1  O3 set to 0.105
Van der Waals radius of atom 63ATP 1  PB set to 0.105
Van der Waals radius of atom 63ATP 1  O2 set to 0.105
Van der Waals radius of atom 63ATP 1  O1 set to 0.105
Van der Waals radius of atom 63ATP 1  O3 set to 0.105
Van der Waals radius of atom 63ATP 1  PA set to 0.105
Van der Waals radius of atom 63ATP 1  O2 set to 0.105
Van der Waals radius of atom 63ATP 1  O1 set to 0.105
Van der Waals radius of atom 63ATP 1  O5 set to 0.105
Van der Waals radius of atom 63ATP 1  C5 set to 0.105
Van der Waals radius of atom 63ATP 1  C4 set to 0.105
Van der Waals radius of atom 63ATP 1  O4 set to 0.105
Van der Waals radius of atom 63ATP 1  C3 set to 0.105
Van der Waals radius of atom 63ATP 1  O3 set to 0.105
Van der Waals radius of atom 63ATP 1  HA set to 0.105
Van der Waals radius of atom 63ATP 1  C2 set to 0.105
Van der Waals radius of atom 63ATP 1  O2 set to 0.105
Van der Waals radius of atom 63ATP 1  HA set to 0.105
Van der Waals radius of atom 63ATP 1  C1 set to 0.105
Van der Waals radius of atom 63ATP 1  N9 set to 0.105
Van der Waals radius of atom 63ATP 1  C8 set to 0.105
Van der Waals radius of atom 63ATP 1  N7 set to 0.105
Van der Waals radius of atom 63ATP 1  C5 set to 0.105
Van der Waals radius of atom 63ATP 1  C4 set to 0.105
Van der Waals radius of atom 63ATP 1  N3 set to 0.105
Van der Waals radius of atom 63ATP 1  C2 set to 0.105
Van der Waals radius of atom 63ATP 1  N1 set to 0.105
Van der Waals radius of atom 63ATP 1  HA set to 0.105
Van der Waals radius of atom 63ATP 1  C6 set to 0.105
Van der Waals radius of atom 63ATP 1  N6 set to 0.105
Van der Waals radius of atom 63ATP 1  HA set to 0.105
Van der Waals radius of atom 63ATP 1  HA set to 0.105
Van der Waals radius of atom 8ATP PG set to 0.105
Van der Waals radius of atom 01ATP PB set to 0.105
Van der Waals radius of atom 01ATP PA set to 0.105
Reading solvent configuration
"216H2O,WATJP01,SPC216,SPC-
MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984"
solvent configuration contains 648 atoms in 216 residues

Initialising van der waals distances...
Will generate new solvent configuration of 3896x1x1 boxes
Generating configuration
Sorting configuration
Found 1 molecule type:
    SOL (   3 atoms): 841536 residues
Calculating Overlap...
box_margin = 0.315
Removed 2232444 atoms that were outside the box
Table routines are used for coulomb: FALSE
Table routines are used for vdw:     FALSE
Cut-off's:   NS: 0.48   Coulomb: 0.48   LJ: 0.48
Generated table with 500 data points for COUL.
Tabscale = 500 points/nm
Generated table with 500 data points for LJ6.
Tabscale = 500 points/nm
Generated table with 500 data points for LJ12.
Tabscale = 500 points/nm
Going to determine what solvent types we have.
There are 0 molecules, 2531860 charge groups and 2531860 atoms
There are 0 optimized solvent molecules on node 0
There are 0 optimized water molecules on node 0
Fatal error: realloc for nl->iinr (40509752 bytes, file 
C:\source\gromacs-3.1.
src\mdlib\ns.c, line 97, nl->iinr=0x0x       0): No such file or 
directory

Mr Raj Badhan
School of Pharmacy and Pharmacetical Science
The University of Manchester
Manchester, UK.