Brief description of tools/files: I am using CHARMM36 forcefield in molecular dynamics computed with GROMACS. In the newest versions of CHARMM36 forcefield in GROMACS format (July 2020 and February 2021) pseudouridine and other atypical RNA nucleotides are not present in merged.rtp files, but the earlier version from March 2019 includes them. Were they deleted or was it just an oversight?
Link: MacKerell Lab (CHARMM36 files in GROMACS format on University of Maryland site)
Contact person (name and email address): -
How the work has been tested/reviewed: -
I have asked the very question on the CHARMM forum and got the answer that in the CHARMM distribution pseudouridine and other atypical RNA nucleotides are present, so it is probably an issue with the forcefield files prepared to use with GROMACS. But I am still not sure why they do not contain pseudouridine and other atypical nucleotides considering these compounds are included in earlier versions.
Thank you in advance for any help.