[gmx-users] CHARMM36 force field available for GROMACS
jim.jim.strong at gmail.com
Mon Mar 10 00:23:39 CET 2014
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.
On Sun, Mar 9, 2014 at 6:34 AM, Justin Lemkul <jalemkul at 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
>> atom name convention. Particularly, why do atoms H2' and H2'' correspond
>> 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 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
> 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-request at gromacs.org.
More information about the gromacs.org_gmx-users