# How to prepare an infinite DNA system?

**URL:** <https://gromacs.bioexcel.eu/t/how-to-prepare-an-infinite-dna-system/3127>\
**Category:** User discussions\
**Created:** [November 11, 2021, 3:19pm UTC](https://gromacs.bioexcel.eu/t/how-to-prepare-an-infinite-dna-system/3127 "2021-11-11T15:19:29Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![kanshrute](https://avatars.discourse-cdn.com/v4/letter/k/7cd45c/32.png) [@kanshrute](https://gromacs.bioexcel.eu/u/kanshrute)\
**Post date:** [November 11, 2021, 3:19pm UTC](https://gromacs.bioexcel.eu/t/how-to-prepare-an-infinite-dna-system/3127/1 "2021-11-11T15:19:29Z")

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GROMACS version: 2021  
GROMACS modification: No

I am currently trying to prepare an infinite ds-ZDNA (across PBC) system.

1. I first built a 12 bp ZDNA from 3DNA and passed it through pdb2gmx to get the .gro and .top file
2. I manually removed the last residues on both ends of the DNA in both the strands in the .top and .gro file
3. I manually changed the bond definitions alone to make sure I maintain periodicity (For instance, I removed the bond entry between 28-O3’ (last O of 1st residue) and 29-P (first P of 2nd residue), replaced 343-O3’ (last O of 11th residue) bonded to 344-P (first P of 12th residue) with 29-P (first P of 2nd residue) and similarly for the other strand). I made no changes to angles/dihedrals etc.(I am not sure how the changes should be made)

However, I am unable to see the long bond connecting the two ends of the strand, across the box when I visualize the modified .gro file after solvent addition in VMD. Could someone help me figure out where I am making a mistake?

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**Author:** ![hess](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/hess/32/416_2.png) [@hess](https://gromacs.bioexcel.eu/u/hess)\
**Post date:** [November 15, 2021, 7:55pm UTC](https://gromacs.bioexcel.eu/t/how-to-prepare-an-infinite-dna-system/3127/2 "2021-11-15T19:55:35Z")

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The best way would to use the cyclic option of pdb2gmx, but unfortunately that does not (yet) support molecules that are cyclic over periodic boundaries. If you can generate a circular DNA structure, you could user that to generate the topology and take the coordinates you already have to start your run.