[gmx-users] tpr without top-file
David van der Spoel
spoel at xray.bmc.uu.se
Mon Oct 4 12:16:59 CEST 2004
On Mon, 2004-10-04 at 11:57, Peter Zoon wrote:
> I've succesfully made a topology with x2top, but I'm still not able to
> get a tpr file from this topfile.
> While running grompp a get a lot of warnings like this:
> WARNING 385 [file "output.top", line 1205]:
> No default Angle types, using zeroes
> When I ignore the warnings finally grompp crashes on
> ERROR: One of the box vectors is shorter than twice the cut-off length.
> Increase the box size or decrease rcoulomb.
> But increasing the box size (I started from a pdb, which has no box
> size? later converted to gro) or decreasing the rcoulomb in the mdp
> doesn't seem to have any effect.
there are three cut-offs. all should be < half the box.
> Any suggestions apart from the ones already mentioned?
> Anton Feenstra wrote:
> > Peter Zoon wrote:
> >> sounds like a good plan, but would this also work for a somewhat more
> >> complicated system?
> >> my system looks more or less like this:
> >> thread= napthalimide-(CH2)12-succinamide-CH2-C-(phenyl)2
> >> the macrocycle consists of a coupleof phenyl rings bonded together
> >> via amide groups.
> >> I think most of the atoms are in ffgmx.n2t so I'll give it a go.
> > Alternatively, it shouldn't be a problem to write your own program (or
> > perl
> > or awk script), that generates a dummy topology, with the proper atom
> > names
> > (which you can read from the .gro file) and only bonds for the
> > connectivity.
> > For the bonds, you'll probably want to parse those out of the topology
> > file
> > you used in your 'other' md program. You'll need to add in fake atom
> > types
> > and fake parameters for the bonds as well, since grompp requires them.
> > I once wrote an amber2gromacs topology converting script (in awk...),
> > which
> > you may want to use as a template. It has the code to write topology
> > files.
> > It should be in the contributions section, otherwise it'll be in the mail
> > list archives somewhere. If that fails, ask me.
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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