[gmx-users] Grompp error "No default Ryckaert-Bell. types"

Justin Lemkul jalemkul at vt.edu
Mon May 4 19:31:37 CEST 2015

On 5/4/15 1:06 PM, Alex wrote:
> JL> 2. As far as bonded interactions are concerned, in the .rtp only [bonds] are
> JL> required to define connectivity.  Remaining bonded interactions are then deduced
> JL> from bond connectivity.  If a directive like [angles] or [dihedrals] is present,
> JL> those values are used, instead.  If an [angles] directive is "missing" that just
> JL> tells pdb2gmx "create all possible angles from the given bonded connectivity."
> Well, yes, but the atomtypes were defined in that rtp and no correct
> triplets or quadruplets were available in ffbonded for those
> combinations. Then, either define directly
> in rtp, or stick them into your ffbonded. Am I missing something here?

I was just clarifying what was a very (to me) confusing exchange.  The 
statements made could easily be taken out of context and misapplied.

"oplsaa seems to look up triplets for [ angles ] elsewhere" is not really right, 
that's what I was explaining about the fundamental way pdb2gmx processes the 
.rtp to write angles and dihedrals.

"The oplsaa version of aminoacids.rtp only lists dihedral and improper angles 
explicitly, and that is exactly what's grompp complaining about in your case." 
As worded, this seems like you're saying that the fact that only dihedrals and 
impropers are listed is the source of the problem.  That's not the case, but 
what you say above is - the parameters for the defined interaction are simply 
not in the force field and therefore must be added.  Of course, if the OP had 
simply Googled the error, this information would have been readily apparent and 
would have saved all involved a lot of typing :)



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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