[gmx-users] Ryckaert-Bellemans Dihedral with AMBER

Justin Lemkul jalemkul at vt.edu
Wed Mar 26 18:45:02 CET 2014

On 3/26/14, 1:30 PM, tarak karmakar wrote:
> Dear All,
> I need to use one Ryckaert-Bellemans dihedral type of a dihedral in a new
> molecule. To do so, I'm including all the coefficients in .rtp file as
> given below, (after bonds section)
> [dihedrals]
>          HX   CX    CX   OX    3  -7.70990 -10.7269 -15.2261 -2.2442
> -0.25839 0.0000
> The Force field I'm using for the protein is the amber99sb-ildn.ff.
> I have  read an old post [
> https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2013-April/080306.html]
> in the mailing list and got some clues about how to use this kind of
> dihedral forms. Accordingly I have approached.
> But at the end I've got the following error,
> "No default Proper Dih. types"
> Do I need to do something more?
> Could anyone guide me the proper way of implementing it?

Are the parameters for that dihedral written to the .top?  A [dihedrals] entry 
in an .rtp file maps to the .top, but normally parameters are not explicitly 
defined in the .rtp.  The parameters are defined in ffbonded.itp and grompp 
looks them up.  If they are present in the .top, there's no reason for grompp to 
(1) go looking for them or (2) think the dihedral is periodic.  Probably the 
conflict comes from the fact that the parent force field is structured for type 
9 periodic dihedrals, but in principle you should be able to add whatever you want.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


More information about the gromacs.org_gmx-users mailing list