VMD-L Mailing List

From: Bikan Tan (btan_at_ncsu.edu)
Date: Mon Aug 08 2011 - 18:59:19 CDT

I am trying to cionize a 2base pair DNA with 2 sodium ion(with no water)
like following:

/home/bikan/lib/vmd/plugins/LINUXAMD64/bin/cionize1.0/cionize -p 8 -i
test.cfg -f pdb 2GC_Bdna.pdb.pdb

and my test.cfg looks like:
****************************************************************************
R_ION_SOLUTE 1.0
BORDERSIZE 10
gridspacing 0.5
r_ion_ion 1.0
XYZDIM -32 -32 -32 32 32 32
SHOWOPT
begin
SAVEGRID savegrid
PLACEION SOD 2 1
SAVEION saveion.pdb
*****************************************************************************
But I am getting this error:
*****************************************************************************
Current options:
        Ion-solute distance: 1.000000
        Ion-Ion distance: 1.000000
        Grid spacing: 0.500000
        Boundary size: 10.000000
        Max. Processors: 8

>>>
Running cionize on input file 2GC_Bdna.pdb.pdb
        Ion-solute distance: 1.000000
        Ion-Ion distance: 1.000000
        Grid spacing: 0.500000
        Boundary size: 10.000000
        Max. Processors: 8
*ERROR: Unable to open input file. Exiting...*

Maximum extents of the considered system (including boundary) are:
        X: -32.000 to 32.000 Y: -32.000 to 32.000 Z: -32.000 to
32.000
Using a grid spacing of 0.500000 angstroms, the grid is 67259781 x
6745399904 x 140735713505040

Allocating memory for data arrays...
        Allocating 0 KB for atom arrays
        Allocating 0 KB for atom grid point array
        Allocating 8073620364246 MB for grid energy array
        Allocating 6416451602165 MB for exclusion array
Error: Failed to allocate memory for data arrays

*****************************************************************************

I am guessing it is because of the pdb file that somehow cionize does not
read happily.(I attached the pdb file)
Could someone please give me some examples on how to cionize?

Thank you so much,
Bikan