[gmx-users] Error in .top when running grompp for final product MD

Mark Abraham mark.abraham at anu.edu.au
Sat Jan 6 15:23:11 CET 2007

> Dear gromacs users,
> I am running MD for a protein with 212 amino acid residues.
> When I run grompp (grompp -f pn_md.mdp -c pn_md.pdb -r pn_md.pdb -p pn.top
> -
> o pn_md.tpr ) for the final product MD, I receive the following error
> message.
> I properly included sol and ion in the temperature control part of
> pn_md.mdp.
> If I include ¡°define = -DPORRES¡± in pn_md.mdp, both grompp and mdrun
> work
> fine.
> The topolofy file pn.top worked well in the previous steps (em.mdp and
> pr.mdp).
> Any suggestions would be appreciated.

Like I said last time in
http://www.gromacs.org/pipermail/gmx-users/2007-January/025262.html, these
symptoms are not being caused by your topology, it's the .mdp file that is


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