[gmx-users] Difference between charmm22 and charmm27 force fields.

[Justin Lemkul]

On 7/3/14, 4:30 PM, Dawid das wrote:
> Dear gromacs experts,
>
> I have a question not related directly to gromacs program.
> Is there difference in parameters for protein (aminoacids) atom types
> between charmm22 and charmm27? In other words, may I use parameters for
> charmm22 for a new non standard aminoacid residue if I use charmm27 for all
> other aminoacids?
>

There is a pervasive nomenclature mistake that people often make.  There is no 
such thing as a CHARMM27 protein force field.  CHARMM27 is a nucleic acid force 
field.  The confusion comes with the fact that when CHARMM27 was released, so 
too was the CHARMM22/CMAP force field for proteins, which introduces the CMAP 
terms on the CHARMM22 force field for better secondary structure sampling.  The 
CHARMM22/CMAP and CHARMM27 force fields are compatible, but technically 
different force fields.  What Gromacs distributes in "charmm27.ff" in terms of 
proteins is actually CHARMM22/CMAP.

So after all that, the real answer is: it's probably fine, because the protein 
force field is actually CHARMM22/CMAP.  If your residue predates the 
introduction of CMAP (i.e. some old parameter set from over 10 years ago), you 
should verify that inclusion of such terms does not cause problems (it 
shouldn't, but you never know).

-Justin

-- 
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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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