[gmx-users] bad box error

[Justin Lemkul]

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
>>
>> --
>> ==============================**==========
>>
>> 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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-- 
========================================

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

========================================