[gmx-users] Genbox error (File input/output error:topol.top)

[Soo J]

 Hi
   I am new to GROMACS.
   
   I intend to do simulation with simple DNA.
   After some manupulation of the original PDB file(with no water), I was able to run
   pdb2gmx  and editconf. After editconf, I tried genbox to solvate the DNA but I got error.
   
   Here is what I did
   > pdb2gmx -missing -f 111.pdb -p 1.top -o 1.gro
 
 > editconf -f 1.gro -o nopbc -d 0.5 -bt dodecahedron -nopbc
 
 Everything is fine and no error so far. But when I tried the following..
 
 > genbox -cp nopbc.gro -cs spc216 -p -o nonopbc
 .....
 .....
 .....
    
Opening library file /usr/share/gromacs/top/aminoacids.dat
Opening library file /usr/share/gromacs/top/atommass.dat
Opening library file /usr/share/gromacs/top/vdwradii.dat
Opening library file /usr/share/gromacs/top/dgsolv.dat
#Entries in atommass.dat: 82 vdwradii.dat: 26 dgsolv.dat: 7
Reading
 solute
 configuration
GROwing Monsters And Cloning Shrimps
Containing 589 atoms in 28 residues
Initialising van der waals distances...
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 3x3x2 boxes
Generating configuration
Sorting configuration
Found 1 molecule type:
    SOL (   3 atoms):  3888 residues
Calculating Overlap...
box_margin = 0.315
Removed 2901 atoms that were outside the box
Neighborsearching with a cut-off of 0.45
Table routines are used for coulomb: FALSE
Table routines are used for vdw:     FALSE
Cut-off's:   NS: 0.45   Coulomb: 0.45   LJ: 0.45
System total charge: 0.000
Neighborsearching with a cut-off of 0.45
Grid: 20 x 20 x 14 cells
Succesfully made neighbourlist
nri = 20651, nrj =
 449052
Checking
 Protein-Solvent overlap: tested 9501 pairs, removed 1134 atoms.
Checking Solvent-Solvent overlap: tested 87594 pairs, removed 1404 atoms.
Added 2075 molecules
Generated solvent containing 6225 atoms in 2075 residues
Writing generated configuration to nopbc_fin.gro

Back Off! I just backed up nopbc_fin.gro to ./#nopbc_fin.gro.3#
GROwing Monsters And Cloning Shrimps

Output configuration contains 6814 atoms in 2103 residues
Volume                 :     73.1608 (nm^3)
Density                :     1043.86 (g/l)
Number of SOL molecules:   2075

Processing topology
-------------------------------------------------------
Program genbox, VERSION 3.3
Source code file: futil.c, line: 340

File input/output error:
topol.top
-------------------------------------------------------

"If You Want Something Done You Have to Do It Yourself" (Highlander II)
   
   
   In the end, I have no topology  file ! 
  Of course if I run genbox without -p option, genbox gives no error but I don't have topology file and I can not run simulation ( Well.. I suppose).
   
   So, what am I doing wrong ? This is my very first GOMACS trial.
   Thank you
   
   Soo 

			
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