[gmx-users] I can't figure out what is wrong with my .gro

[Justin Lemkul]

On 1/9/13 8:02 PM, Xu Dong Huang wrote:
> Oh, you have an Additional line after vector size box…. I thought you said to remove that blank line
>

There is no additional line.  The last line in the file must be the box vectors.

-Justin

> Xu Dong Huang
> Chemical & Biochemical Engineering
> Rutgers School of Engineering
> xudongh at eden.rutgers.edu
>
> On Jan 9, 2013, at 7:58 PM, Xu Dong Huang <xudongh at eden.rutgers.edu> wrote:
>
>> @Justin,
>>
>> I did that, and it still says I have 103.
>>
>> Xu Dong Huang
>> Chemical & Biochemical Engineering
>> Rutgers School of Engineering
>> xudongh at eden.rutgers.edu
>>
>> On Jan 9, 2013, at 7:49 PM, Xu Dong Huang <xudongh at eden.rutgers.edu> wrote:
>>
>>> @Justin,
>>>
>>> I did what you suggested, and I still can't load my molecule in VMD. Maybe I am still doing something wrong with the new line character thing.
>>>
>>>
>>> Xu Dong Huang
>>> Chemical & Biochemical Engineering
>>> Rutgers School of Engineering
>>> xudongh at eden.rutgers.edu
>>>
>>> On Jan 9, 2013, at 7:22 PM, Xu Dong Huang <xudongh at eden.rutgers.edu> wrote:
>>>
>>>> @ Justin,
>>>>
>>>> I laughed. :) Thank you. I can't believe I miss the smallest and most rudimentary things.
>>>> Thanks again,
>>>> Xu Dong Huang
>>>> Chemical & Biochemical Engineering
>>>> Rutgers School of Engineering
>>>> xudongh at eden.rutgers.edu
>>>>
>>>> On Jan 9, 2013, at 7:20 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>>>
>>>>>
>>>>>
>>>>> On 1/9/13 7:16 PM, Xu Dong Huang wrote:
>>>>>> @ Justin,
>>>>>>
>>>>>> Thanks for always saving me from my mistakes. But I don't quite understand what is a new line character?
>>>>>>
>>>>>
>>>>> The thing you get when you press enter.
>>>>>
>>>>> http://en.wikipedia.org/wiki/Newline#In_programming_languages
>>>>>
>>>>> Note that Google has plenty more to say ;)
>>>>>
>>>>> There should not be a blank line at the end of the .gro file, though, but to be correctly parsed by VMD, the line must terminate with a '\n' character.  So at the end of your box vector line, hit return then backspace.
>>>>>
>>>>> -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
>>>>>
>>>>> ========================================
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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

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