[gmx-users] Grompp error "No default Ryckaert-Bell. types"
jalemkul at vt.edu
Mon May 4 13:35:21 CEST 2015
On 5/4/15 4:20 AM, Alex wrote:
> The rtp file format and its acceptable entries are not forcefield-specific
> (oplsaa seems to look up triplets for [ angles ] elsewhere), I just wanted to
> give an example of that.
> 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.
I seem to be only getting half of the messages in this conversation, but let me
clear a few things up:
1. The errors about missing R-B parameters have nothing to do with "missing"
angles in the .rtp. R-B are dihedrals, so that's not what grompp is complaining
2. As far as bonded interactions are concerned, in the .rtp only [bonds] are
required to define connectivity. Remaining bonded interactions are then deduced
from bond connectivity. If a directive like [angles] or [dihedrals] is present,
those values are used, instead. If an [angles] directive is "missing" that just
tells pdb2gmx "create all possible angles from the given bonded connectivity."
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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