[gmx-users] Problems using grompp and amber force field
mario at exactas.unlpam.edu.ar
Wed May 9 20:57:09 CEST 2007
Thanks everybody by the comments.
There was a error in the include files of the topology: The itp file
generated by pdb2gmx program was localized in a different folder that
where we were running to the grompp program.
El mar, 08-05-2007 a las 02:05 +0100, TJ Piggot escribió:
> With regards to the versions you are correct, ffamber_v3.3.1 is for use
> with Gromacs 3.3.1. As for the error i would suggest you do what Mark says
> and make sure all your inclusions are correct. If you still can't find the
> problem then you need to post some of your .top file so we can have a look
> at it
> --On 08 May 2007 10:53 +1000 Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> > root wrote:
> >> Dear GROMACS user:
> >> Erik and Tom thanks by the comments, too. Sorry, I read the FAQ pages of
> >> http://folding.stanford.edu and now I understand your comments.
> >> We tried with cpp = /lib/cpp -traditional in the mdp file. The warning
> >> desapears, but the error messages is similar.
> >> (Fatal error:
> >>>>> Atoms in the .top are not numbered consecutively from 1
> >>>>> -------------------------------------------------------
> >>>>> We tested the dick.top file, and we verified that the atoms
> >>>> are numbered
> >>>>> consecutively from 1 to 758.)
> > Have you inspected the #included files as well? The way cpp works, any
> > file #included is literally dropped into its parent file, so if you had
> > something wrong in such an #inclusion you'd need to fix that.
> > Mark
> > _______________________________________________
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> TJ Piggot
> t.piggot at bristol.ac.uk
> University of Bristol, UK.
> gmx-users mailing list gmx-users at gromacs.org
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