Pdb file with the bond connection information

User discussions
1

GROMACS version: 2022
GROMACS modification: Yes/No
Hello, Gromacs users.

I attempted to replicate molecules with recurring patterns in the XY planes. I generate .itp files that account for intermolecular bonds, angles, and dihedrals while taking into consideration the periodic boundary conditions (PBC). However, when I save my coordinates in a gro/pdb file for further analysis, I want data on the bond connections. Can this information be included in a pdb file or is there a method to convert the Gromacs tpr file to mol or mol2 files that include information on bonds across PBC?

Best regards

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There’s a function in Gromologist to add CONECT entries to any structure, and then save as PDB. I added an extra feature to include PBC if asked with pbc=True, although this can be slow for large systems as it falls back to the naive distance calculation algorithm.

One option in that case is to first save a subset of the full system, and then add CONECT only to that structure.

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Hello @milosz.wieczor ,
Thank you for your help.
I will try to do this.