[gmx-users] No default Proper Dih. types

Dusan d.petrovic at fz-juelich.de
Sat Aug 8 10:05:11 CEST 2015


I have a similar problem. Recently I tried to implement a functionalized Cys 
residue into the amber99sb-ildn.

I added a new residue into aminoacids.rtp, aminoacids.hdb, I defined 
everything new in atomtypes.atp and ffnonbonded.itp, and I added in 
necessary [ bondtypes ], [ angletypes ], and [ dihedraltypes ] into ffbonded.itp.

I got topology from the Acpype, so my proper dihedrals are of the 
RB type (func. = 3). So, in ffbonded.itp after [ dihedraltypes ] section from 
the original ff, I added my new [ dihedraltypes ] section with the RB 
dihedrals from the acpype which was followed by the impropers 
[ dihedraltypes ] section.

However, after running grompp, I get the following message:

ERROR 1 [file topol.top, line 46579]:
  No default Angle types

ERROR 2 [file topol.top, line 66304]:
  No default Proper Dih. types

There is only one error for the angles (though I check and the 
angle of these atomtypes was explicitly defined in ffbonded.itp.

There are, however, many errors concerning the dihedrals. Can it 
be because I'm using RBs? Or maybe my order was wrong so 
Gromacs can't read it?

Thanks for any help.

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