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

[Caterina Arcangeli]

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

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