[gmx-users] editconf/genbox problem in Gromacs 4.0

[Xavier Periole]

On Fri, 7 Nov 2008 11:23:14 +0100
  "Caterina Arcangeli" <caterina.arcangeli at casaccia.enea.it> wrote:
> Dear gmx-users,
> 
> I have encountered a similar editconf/genbox problem posted by Matt
> Danielson on 14 October:
> I 'm using Gromacs 4.0 (installed on MacOS).
> 
> 1. editconf -f my_protein.pdb -bt dodecahedron -d 0.9 -c -o 
>may_protein_box.pdb
use gro files for output and it works. The box size is not written
in the pdb file, although it used to be.
> 
> The output from editconf does not report errors, but I noted that the
> volume of the box is 0!
> 
> ----------- output message-------------------------------
> WARNING: masses will be determined based on residue and atom names,
>         this can deviate from the real mass of the atom type
> Entries in atommass.dat: 178
> WARNING: vdwradii will be determined based on residue and atom names,
>         this can deviate from the real mass of the atom type
> Entries in vdwradii.dat: 28
> Entries in dgsolv.dat: 7
> Entries in electroneg.dat: 71
> Entries in elements.dat: 218
> Read 16824 atoms
> Volume: 0 nm^3, corresponds to roughly 0 electrons
> -----------------------------------------------------------------
> 
> 2. genbox_d -cp my_protein_box.pdb -cs spc216.gro  -o
> my_protein_wat.pdb -p my_protein.top
> 
> The output from genbox_d reports the following error:
> -------------------------------------------------------
> Program genbox, VERSION 4.0
> Source code file: gmx_genbox.c, line: 744
> 
>Fatal error:
> Undefined solute box.
> Create one with editconf or give explicit -box command line option
> -------------------------------------------------------
> 
> 
> I have performed the same commands on another machine (Linux) running
> version 3.3 and I produced with success a nice solvent box.
> 
> Suggestions?
> 
> Thanks,
> Caterina
> 
> 
> 
> -- 
> Caterina Arcangeli
> ENEA, Dept. Physics (FIM-CAMO)
> C.R. Casaccia, SP 026
> Via Anguillarese 301 - 00123 Roma
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-----------------------------------------------------
XAvier Periole - PhD

- Molecular Dynamics Group -
NMR and Computation
University of Groningen
The Netherlands
-----------------------------------------------------