[gmx-users] bad box error

[amna khan]

i am using the best conformation of protein ligand file obtained after
docking results

i made the .gro file  by
 pdb2gmx -f pro.pdb -o proceed.gro -water spc -missing -ignh

then the ligand codinates from ligand,gro was obtained from prodrug sever,
then i pasted ligand coordinates in this file
the first three lines are

Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
 2059
  705SER      N    1  -3.373  -1.131   1.295
  705SER     H1    2  -3.442  -1.166   1.232
  705SER     H2    3  -3.339  -1.043   1.261
  705SER     H3    4  -3.298  -1.196   1.303

last three lines are
    1LIG  OAR     33   0.425  -0.911   1.194
    1LIG  CAC     34   0.593  -1.073   1.167
    1LIG  CAT     35   0.500  -1.191   1.198
   9.21266   2.49507   2.95990




and the output for command is
wc -l proceed.gro
2100 proceed.gro



On Wed, Jan 30, 2013 at 1:20 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 1/29/13 3:07 PM, amna khan wrote:
>
>> so, i could i correct this ?
>>
>>
> Probably, but we need a lot more information if you want help:
>
> 1. Describe what your system is and how you constructed conf.gro
> 2. Post the first 3 and last 3 lines of conf.gro
> 3. Post the output of wc -l conf.gro
>
> -Justin
>
>
>>
>> On Wed, Jan 30, 2013 at 12:52 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>>
>>> On 1/29/13 2:43 PM, az kalsom wrote:
>>>
>>>  hi ,
>>>>
>>>> when i use "editconf" to generate a dodecahedron box with the command
>>>>
>>>> editconf -f conf.gro -o newbox.gro -bt dodecahedron -d 1.0
>>>>
>>>> the output shows the warning
>>>>
>>>> bad box in file
>>>>
>>>> generated  a new cubic box  9.213 x    2.495 x    2.960
>>>>
>>>>
>>>> what is the mean of "bad box in file"?
>>>>    and why editconf generates a cubic box?
>>>>
>>>>
>>>>  Whatever input you have provided is malformatted.
>>>
>>> -Justin
>>>
>>> --
>>> ==============================****==========
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> ==============================**==========
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
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