[gmx-users] editconf/genbox problem in Gromacs 4.0
Berk Hess
gmx3 at hotmail.com
Fri Nov 7 11:44:11 CET 2008
Hi,
This is a known bug in 4.0.
It has been fixed for 4.0.1, which will hopefully be released today.
Berk
> Date: Fri, 7 Nov 2008 11:23:14 +0100
> From: caterina.arcangeli at casaccia.enea.it
> To: gmx-users at gromacs.org
> Subject: [gmx-users] editconf/genbox problem in Gromacs 4.0
>
> 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
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