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

[jantonioms J. A. Mondragon S]

it seems there's a problem with my compiler. I succesfully run grompp
in another computer with
gromacs distribution. I compare and check the two ggc version.

On Nov 9, 2007 7:10 PM, Mark Abraham <mark.abraham at anu.edu.au> wrote:
>
> > 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
>
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