[gmx-users] CHARMM36 force field available for GROMACS

[Jim]

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 <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
>> 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
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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