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

[Tsjerk Wassenaar]

Hi Soo,

To start with, you have to supply the topology generated with pdb2gmx to
genbox. The option -p defaults to topol.top, but you named your topology
1.top. Therefore genbox complains that there's no topol.top and you should
give -p 1.top instead.

In addition, one thing struck me in your sequence of commands. You used
pdb2gmx -missing. Why is that? Do you know what it does? It ignores missing
atoms if they aren't listed in the pdb file. If atoms are indeed missing,
it's a very good recipe for crashing a simulation. And why are you using
editconf with the option -nopbc? That's pointless unless you hand topology
information to editconf (a .tpr file) which it can use to make your molecule
whole, in case it is broken. I would expect that the pdb file doesn't
contain a broken molecule; it won't if it's from an experimentally
determined structure or the direct result of a simulation with gromacs.

Cheers,

Tsjerk

On 12/14/05, Soo J <icarustiki at yahoo.com> wrote:
>
>  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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--

Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336
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