[gmx-users] CHARMM36 force field available for GROMACS

jim jim.jim.strong at gmail.com
Sun Mar 9 11:29:35 CET 2014

I'm confused about the existence of H5'1 and H5'2 atom names in the RNA
nucleotides (in merge.rtp). I thought all atom names followed the CHARMM 36
atom name convention. Particularly, why do atoms H2' and H2'' correspond to
the latter, while H5'1 and H5'2 carry the same name as the Gromacs
convention? At the same time, in [bonds] H5' and H5'' are used instead of
H5'1 and H5'2. I suspect H5'1 and H5'2 should have been H5' and H5''.

On the other hand, I assume H5'1 and H5'2 are correct for the DNA since
there is a correspondence with H2'1 and H2'2. 

Or am I missing anything?


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