[gmx-users] query regarding a topology file

Jagannath Mondal jmondal at chem.wisc.edu
Thu Apr 12 18:31:48 CEST 2007

     I am trying to prepare a gromacs topology file for a non-natural  
peptide. For that I prepared a molecule.itp file and a corresponding  
ff***bon.itp file which contains all the bond-type, angle-type and  
  But, when I try to use
grompp for generating the .tpr file, it shows the following statement 
(But these are not 'warnings') . The following terms are atom indices  
and they are implying RB dihedrals.

Skip RB 204 206 208 209 (zero contribution)
Skip RB 207 206 208 209 (zero contribution)
Skip RB 207 206 208 210 (zero contribution)
Skip RB 207 206 208 213 (zero contribution)
  skip   RB 211 210 229 230(zero contribution)
But the corresponding dihedral types are present in the ff**bon.itp  
file.(For example 211 210 229 230 implies HB CT2  C O),  But still  
why is it skipping those dihedrals ?  previously, if it could not  
find any dihedral type it used to
give an warning for not showing that, But In this case, it is  
skipping some dihedral types though they are present in the   
ff***bon.itp file.   Can you say  whether this is a serious error or  
it is OK?
    Jagannath Mondal

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