[gmx-users] CHARMM36 force field available for GROMACS

Justin Lemkul 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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