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

[Mark Abraham]

> 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?

I don't know if it is the cause of the problem, but backslashes are not
usually interpreted as directory & file separators on Unix - unlike
Windows. Use forward slashes. As a first guess, I'd say that cpp is
interpreting your include directive with the backslashes starting escape
sequences for funky meanings, hence failing to find ffamber. That assumes
you've put ffamber in that location, of course! :-)

Mark