GROMACS version: 2023
GROMACS modification: No
Hi, I hope you’re doing well.
Is it necessary to remove ions and crystallographic waters from a DNA PDB file downloaded from RCSB before generating the topology?
According to the protocol outlined in the following paper, this step was not performed for a protein.
There is no standard procedure here; it depends on the system. Are the ions functionally important? Or are they an artifact of some crystallization buffer? Are the crystal waters relevant (as in an enzyme active site) or incidental? There’s no harm in keeping them but in most cases they’re going to diffuse away as soon as equilibration starts.
Hi Dr. Lemkul,
Thank you for your response.
I have another question. I recently came across this paper (DOI: 10.1021/acs.jpcb.9b09106) and would appreciate your opinion on the suitability of the CHARMM36 force field for studying interactions between DNA and peptides, as well as DNA and membranes, on the microsecond timescale.
Looking forward to your insights!
For proteins, if there are issues with CHARMM36 over long time scales, AMBER is a reasonable option, but for anything with lipids, CHARMM36 is superior to other atomistic force fields. I know that’s a conundrum if you’re looking for consistency among the different simulations, but that’s where things are at for the moment.
Thank you, Dr. Lemkul, for your detailed response and valuable insights.