How to prepare an infinite DNA system?

User discussions
1

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?

2

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.