[gmx-users] Bad box in protein.gro

[Justin A. Lemkul]

sai nitin wrote:
> 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..
> 

Did you remember to increment the number of atoms on the second line of the .gro 
file after adding the ligand?

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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