Atypical nucleotides missing in the newest versions of CHARMM36

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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.

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This was an inadvertent omission due to (too many) manual steps in the conversion process, which I aim to make better this summer. For now, you can just replace merged.rtp from the feb2021 version with the older one (jul2020). The only relevant change was addition of some missing NBFIXes, not introduction/modification of residue definitions.

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Thank you for the reply. To my eye version from July 2020 does not include pseudouridine. The latest one containing this and other atypical RNA nucleotides was released in March 2019. So in that case does your solution work as well if I use merged.rtp from mar2019?

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OK, sorry for the confusion - someone had recently contacted us to say the modified nucleotides were in the July 2020 version but not the latest; obviously that was incorrect. I would not copy the merged.rtp file from March 2019 and use it as it contains erroneous bonds between atoms and lone pairs for halogenated model compounds (this is an unresolved issue as pdb2gmx cannot handle lone pairs like this…yet) and there are many other updates that have happened in the last two years. If you contact me via email, I can send you an updated force field port but we are not likely to release an official, new port until August when the force field itself is updated.

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Thank you very much! I have sent you an email. I would be grateful for sharing with me an updated version of the forcefield with modified nucleoties.