Thanks for the clarification. *Bonds involving H5' and H5'' in RNA residues should indeed be changed to the H5'1 and H5'2 nomenclature.*
Even though H5' and H5'' are connected to the same atom, what would be the problem to keep these H atom names H5' and H5'' instead of changing them to H5'1 and H5'2? Also, what is the significance of the -O3' P bond listed in the [bonds] of the RNA nucleotides in the previous CHARMM 27 FF? It is absent in CHARMM 36. Thanks. On Sun, Mar 9, 2014 at 6:34 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > 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 nomenclature. > > 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 > > -- > ================================================== > > 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 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > ================================================== > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.