# ssDNA binding to Carbon Nanotube

**URL:** <https://gromacs.bioexcel.eu/t/ssdna-binding-to-carbon-nanotube/1648>\
**Category:** User discussions\
**Created:** [February 26, 2021, 9:29pm UTC](https://gromacs.bioexcel.eu/t/ssdna-binding-to-carbon-nanotube/1648 "2021-02-26T21:29:39Z")\
**Posts on this page:** 6\
**Page:** 1

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**Author:** ![sparsh282](https://avatars.discourse-cdn.com/v4/letter/s/e47c2d/32.png) [@sparsh282](https://gromacs.bioexcel.eu/u/sparsh282)\
**Post date:** [February 26, 2021, 9:29pm UTC](https://gromacs.bioexcel.eu/t/ssdna-binding-to-carbon-nanotube/1648/1 "2021-02-26T21:29:39Z")

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GROMACS version:  
GROMACS modification: Yes/No  
Here post your question  
I am trying to simulate binding of ssDNA to the Carbon nanotube however, I ran into the following problems-

1. I can’t find a way to generate a pdb file for a ssDNA.
2. I have been able to simulate nanotube in water using GROMACS but couldn’t figure out how to add another molecule.

I am very new to this field any help will be sincerely appreciated.

Thanks,  
Sparsh

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**Author:** ![JonahC](https://avatars.discourse-cdn.com/v4/letter/j/71c47a/32.png) [@JonahC](https://gromacs.bioexcel.eu/u/JonahC)\
**Post date:** [March 3, 2021, 3:23pm UTC](https://gromacs.bioexcel.eu/t/ssdna-binding-to-carbon-nanotube/1648/2 "2021-03-03T15:23:19Z")

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Hi Sparsh,

For making the ssDNA models, there are a few ways to do it, if it just needs to be a single chain you could use 3DNA;  
[http://web.x3dna.org/custom/option](http://web.x3dna.org/custom/option)

For adding another molecule, you can check tutorial 5 here;  
[http://www.mdtutorials.com/gmx/index.html](http://www.mdtutorials.com/gmx/index.html)

Hope that helps

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<div class="post-metadata">

**Author:** ![sparsh282](https://avatars.discourse-cdn.com/v4/letter/s/e47c2d/32.png) [@sparsh282](https://gromacs.bioexcel.eu/u/sparsh282)\
**Post date:** [March 3, 2021, 4:31pm UTC](https://gromacs.bioexcel.eu/t/ssdna-binding-to-carbon-nanotube/1648/3 "2021-03-03T16:31:06Z")

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Hi Jonah,

Thanks for the help.

What are the other ways to generate pdb files for ssDNA ?

Just want to know the other tools so that I can use them in other projects as well.

Thanks,  
Sparsh

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**Author:** ![JonahC](https://avatars.discourse-cdn.com/v4/letter/j/71c47a/32.png) [@JonahC](https://gromacs.bioexcel.eu/u/JonahC)\
**Post date:** [March 4, 2021, 1:28pm UTC](https://gromacs.bioexcel.eu/t/ssdna-binding-to-carbon-nanotube/1648/4 "2021-03-04T13:28:59Z")

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Sure, I tend to design my DNA in cadnano, then use the cadnano2pdb.py script to convert it, but that is usually for more structured DNA. You could also use the NAB module of Amber

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<div class="post-metadata">

**Author:** ![sparsh282](https://avatars.discourse-cdn.com/v4/letter/s/e47c2d/32.png) [@sparsh282](https://gromacs.bioexcel.eu/u/sparsh282)\
**Post date:** [April 9, 2021, 4:03am UTC](https://gromacs.bioexcel.eu/t/ssdna-binding-to-carbon-nanotube/1648/5 "2021-04-09T04:03:37Z")

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Jonah,

The x3DNA website asks for .parm or .txt file for the DNA sequence. Is there a way to generate these files?

Thanks again for the help,  
Sparsh

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**Author:** ![JonahC](https://avatars.discourse-cdn.com/v4/letter/j/71c47a/32.png) [@JonahC](https://gromacs.bioexcel.eu/u/JonahC)\
**Post date:** [October 29, 2021, 9:10am UTC](https://gromacs.bioexcel.eu/t/ssdna-binding-to-carbon-nanotube/1648/6 "2021-10-29T09:10:17Z")

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Hi Sparsh,  
Sorry I missed this for so long. I’ve not much experience with .parm files, but for .txt files you can just use a text editor such as nano, vim or gedit (or notepad) and write in the bases you want,  
All the best,  
Jonah