I am trying to write custom particles to a PDB file for coarse grain molecular dynamic simulations in GROMACS. In particular, I am trying to model RNA nucleotides using a handful of beads per nucleotide to represent the full atom set. As such, the atoms I am writing to the PDB files are not atoms per say, though they have the usual parameters seen in normal atoms (mass, location, charge, etc.).
Biopython and GitHub packages (forgi in particular) have not been fruitful, as the only atoms I can seem to write correctly to files are standard atoms, and not custom parameter beads used in coarse grain models. If anyone knows how to use these (or other packages) to output PDBs with coarse grain models correctly, that would be extremely helpful.
Have you tried with Martini?
http://cgmartini.nl/index.php/tutorials-general-introduction/tutorial-martini-dna
- Badges
- Science topic