unanswered Martini2 RNA Backbone Dihedrals duplicate atom index error

  • subha
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3 months 1 week ago #9363 by subha
I was trying to coarse grain RNA using Martini2 RNA Model. I found that the RNA Bacbone dihedrals have been defined using duplicate beads For example,

Beads ; type ;equilibrium distance ;force.c ;multiplicity
BB1 BB2 BB3 BB1 2 0 3.5 1
BB2 BB3 BB1 BB2 1 0.04 1 1
BB3 BB1 BB2 BB3 9 -10.02 1.5 2
BB3 BB1 BB2 BB3 9 10.02 1.5 2

As a result the resulting molecule.itp file has duplicate atom indices in and I am getting the error : Duplicate atom index in dihedrals when the molecule.itp file is being read by grompp. Shouldn't dihedrals have all distinct points? Any suggestions would be great. Thanks!

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