[gmx-users] CHARMM36 force field available for GROMACS

Justin Lemkul jalemkul at vt.edu
Sun Mar 9 14:35:58 CET 2014

On 3/9/14, 6:28 AM, jim wrote:
> 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.

What we tried to do was make the fewest changes possible to CHARMM nomenclature, 
while still playing nice the the Gromacs .hdb and .tdb machinery.  You are 
correct in noting the error in the [bonds] involving H5' and H5'' for RNA - I 
will see that this problem is fixed in our next release.  Bonds involving H5' 
and H5'' in RNA residues should indeed be changed to the H5'1 and H5'2 

The H2' and H2'' used in RNA are correct.  Since H2'' is bonded to C2' and H2' 
is bonded to O2', there is no issue in .hdb generation that leads to any 
problem, so those names were left untouched.  Since, in DNA, H2' and H2'' are 
both bonded to C2', they needed to be renamed.

Please let me know if you spot anything else that is unusual or incorrect.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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