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

[Justin Lemkul]

On 1/9/13 8:06 PM, Xu Dong Huang wrote:
> Dear Justin Lemkul,
>
> I had a correspondence with you several times in January about .gro file
> formatting and I remember you suggested to me that there is a code you can use
> in C to automate the spacing format in .gro file generation. I can no longer
> locate that specific email and I was wondering if you could be kind and
> enlighten me again on this format automation procedure in C environment.
>

http://manual.gromacs.org/online/gro.html

-Justin

> Thanks,
>
>
> Xu Dong Huang
> Chemical & Biochemical Engineering
> Rutgers School of Engineering
> xudongh at eden.rutgers.edu <mailto:xudongh at eden.rutgers.edu>
>
> On Jan 9, 2013, at 8:04 PM, Justin Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
>
>>
>>
>> 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 <mailto:xudongh at eden.rutgers.edu>
>>>
>>> On Jan 9, 2013, at 7:58 PM, Xu Dong Huang <xudongh at eden.rutgers.edu
>>> <mailto: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 <mailto: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 <http://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

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