[gmx-users] grompp error

Justin Lemkul jalemkul at vt.edu
Mon Sep 14 12:43:19 CEST 2015

On 9/14/15 4:30 AM, faride badalkhani wrote:
> Dear GROMACS users,
> I need to simulate a hyper branched polymer (a polyamidoamine dendrimer). I
> used the GROMOS53A6 to perform the simulation. But, I have a problem with
> defining the angles and dihedrals that are between two residues (because of
> dendrimers hyper branched structure). I can perform pdb2gmx and solvation,
> but When I run grompp, I got this error " No default Proper Dih. types",

So here the force field doesn't support whatever dihedral(s) that grompp finds.

> and ''Duplicate atom index (...) in dihedrals''. How should I figure it
> out?

Here your topology is set up incorrectly, as the same atom is repeated in a 
given dihedral definition.



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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