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."
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