[gmx-users] CHARMM36 force field available for GROMACS
jalemkul at vt.edu
Mon Mar 10 01:02:31 CET 2014
On 3/9/14, 7:23 PM, Jim wrote:
> 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?
In principle, no, the CHARMM-specific names should work fine, but only if you
add corresponding entries in the merged.arn file to translate between CHARMM and
Gromacs nomenclature. We made the naming change to interface smoothly with the
Gromacs hydrogen-generation (.hdb) mechanism. If you have a coordinate file
that complies with CHARMM naming, i.e. from CHARMM-GUI, then simple sed
statements take care of any issues.
> 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.
+ and - indicate bonds to succeeding and preceding residues, respectively. The
"-O3' P" bond indicates a connection to the previous nucleotide. Since we
produced CHARMM36 directly from CHARMM files, the nomenclature is different and
the bonds are now "O3' +P" instead, which is what CHARMM .rtf files use. It
accomplishes the same thing.
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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