[gmx-users] Grompp error "No default Ryckaert-Bell. types"
nedomacho at gmail.com
Mon May 4 19:47:39 CEST 2015
True, thats why i mentioned Mark.:-) In all honesty, though, for small
molecules, i would prefer to ignore the new format and actually add
everything in the rtp entry to make ffbonded look like less of a zoo.
Also, it was late night of extreme gromacs intercourse for me, which
finally paid off. :-)
On May 4, 2015 11:31 AM, "Justin Lemkul" <jalemkul at vt.edu> wrote:
> 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
>> 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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