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
xudo...@eden.rutgers.edu <mailto:xudo...@eden.rutgers.edu>
On Jan 9, 2013, at 8:04 PM, Justin Lemkul <jalem...@vt.edu
<mailto:jalem...@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
xudo...@eden.rutgers.edu <mailto:xudo...@eden.rutgers.edu>
On Jan 9, 2013, at 7:58 PM, Xu Dong Huang <xudo...@eden.rutgers.edu
<mailto:xudo...@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
xudo...@eden.rutgers.edu <mailto:xudo...@eden.rutgers.edu>
On Jan 9, 2013, at 7:49 PM, Xu Dong Huang <xudo...@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
xudo...@eden.rutgers.edu
On Jan 9, 2013, at 7:22 PM, Xu Dong Huang <xudo...@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
xudo...@eden.rutgers.edu
On Jan 9, 2013, at 7:20 PM, Justin Lemkul <jalem...@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
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