[gmx-users] bad box in protein.gro

Tsjerk Wassenaar tsjerkw at gmail.com
Mon Nov 10 11:32:46 CET 2008

Hi Alessandro,

editconf encounters a bad box in the input file and I think it first
replaces that with a standard box internally. Check the box at the end
of box.gro to see if the result is what it should be (nine numbers,
according to the specification of the rhombic dodecahedon in Chapter 3
of the manual).



On 11/10/08, Alessandro Casoni <alessandro.casoni at unimi.it> wrote:
> Hi all,
>  when i use "editconf" to generate a dodecahedron box with the command:
>  editconf -f protein.gro -bt dodecahedron -o box.gro -d 0.9
>  the output  show me the  following message:
>  .....
>  WARNING 1 [file aminoacids.dat, line 1]:
>   Bad box in file protein.gro
>  Generated a cubic box    6.941 x    4.939 x    7.460
>  .....
>  what is the mean of "bad box in file"?
>  and why editconf generates a cubic box?
>  I use gromacs 4.0
>  regards,
>  Alessandro
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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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