[gmx-users] grompp doesn't process topology file of a DNA fragment using ffamber ports for gromacs

jantonioms J. A. Mondragon S jantonioms at gmail.com
Sat Nov 10 02:04:59 CET 2007

I installed ffamber ports for gromacs, generated gro and topology
files for a DNA structure with pdb2gmx, a box with editconf and added
solvation with genbox. When I try to run grompp i obtain these errors:

checking input for internal consistency...
calling cpp -traditional...
processing topology...
Generated 2628 of the 2628 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 2628 of the 2628 1-4 parameter combinations
ERROR 0 [file "gr_Nast.top", line 761]:
  No default Bond types
ERROR 0 [file "gr_Nast.top", line 3352]:
  No default Angle types
ERROR 0 [file "gr_Nast.top", line 3354]:
  No default Angle types

It seems gromacs don't read ffamber* force field information, however
i using the directive

include = -I\home\jantonioms\Programs\gromacs\share\gromacs\top

in *.mdp file

Can anyone have an idea?

Thanks for help.

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