[gmx-users] Bad box in protein.gro

sai nitin sainitin7 at gmail.com
Wed Apr 4 11:06:24 CEST 2012

Hi all,

I recently started molecular dynamics with gromacs performing
protein-ligand simulations for my project first i worked out example from
justin tutorials on protein ligand system and trying to apply to my protein
and ligand.

First i generated topology for my protein using pdbgmx and then i used
PRODRG tool ligand topology has been generated then i included ligand.itp
file in topol.top file and pasted ligand.gro which is generated from PRODRG
tool in protein.gro as suggested in tutorial but problem comes now
while running editconf as follows warning bad box

editconf -f protein .gro -o box.gro -bt cubic -d 1.0

*WARNING: Bad box in file protein.gro*

Generated a cubic box    5.553 x    4.382 x    4.434
Read 2053 atoms
Volume: 107.894 nm^3, corresponds to roughly 48500 electrons
No velocities found
    system size :  5.553  4.382  4.434 (nm)
    diameter    :  6.093               (nm)
    center      :  0.068 -0.079  0.153 (nm)
    box vectors :  5.553  4.382  4.434 (nm)
    box angles  :  90.00  90.00  90.00 (degrees)
    box volume  : 107.89               (nm^3)
    shift       :  3.978  4.126  3.894 (nm)
new center      :  4.047  4.047  4.047 (nm)
new box vectors :  8.093  8.093  8.093 (nm)
new box angles  :  90.00  90.00  90.00 (degrees)
new box volume  : 530.06               (nm^3)

Actually this problem is already been raised from some one else in gromacs
discussion list i tried to use that solution but it is not helping me

Can any body tell me where i am going wrong..

Thanks in advance

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