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

[Xu Dong Huang]

Must be something wrong with my editor program (BBEdit), because when I open the file you sent me, it shows me there an additional blank line. Ok, time to switch to regular text editor… 


Xu Dong Huang
Chemical & Biochemical Engineering
Rutgers School of Engineering 
xudongh at eden.rutgers.edu 

On Jan 9, 2013, at 8:04 PM, Justin Lemkul <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
>> 
>> 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
> 
> ========================================
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