[gmx-users] No default Bond types error despite entry in ffbonded.itp

[Irem Altan]

Hi all,

I’m trying to add the topology for sucrose manually to the force field, using the .itp file provided here: http://atb.uq.edu.au/molecule.py?molid=22625#panel-md

I created the box with a sucrose molecule and with some waters, and tried to create a .tpr for energy minimization. However, this gives me the error (and similar ones for all bonds, angles, and dihedrals):

ERROR 1 [file topol.top<http://topol.top>, line 79]:
  No default Bond types


Line 79 refers to the bond between the 1st and the 2nd atom, which are types HC and C, respectively. So I added this bond to ffbonded.itp, using the info provided in the link to the ATB database above:

  HC C          2    0.1090    1.2300e+07 ; sucrose HC-C

However, I still get the same error. What am I missing?

Best,
Irem