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 -- ================================================== 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 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul ================================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
