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

[Justin Lemkul]

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 
about.
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

-- 
==================================================

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
http://mackerell.umaryland.edu/~jalemkul

==================================================