Antwort: [CP2K:3344] ERROR in topology_generate_molecule

marco.stenta marco.... at
Thu Jun 30 22:33:43 UTC 2011

Hi everyone,
I was not able to find the keyword REORDERING either (the best way I
know is the google search engine of the berlios website), but I've
found instead

Not impossible to find but, if I may say, the error message referring
to REORDERING was slightly misleading.

The error message itself gives a clue for sure but we had to figure
out what the problem was, as Papy said.

Let me just clarify this (solved) issue for the benefit of other
1) we have an AMBER topology: no segments specification available as
in the PSF
2) molecules are identified with the chains starting from Nterm to
3) we have a Zinc finger with a bounded parametrization: metal and
ligand charge rescaled and bonds between the metal and the
coordinating residues (MTK++ protocol by K. M. Merz)
4) the zinc does not belong to the protein chain, but it is assigned
to a separate molecule by CP2K
5) the zinc is thus bound to residues in the middle of the chain but
it is placed after the end of it: from here the error message: ZN
belongs the same molecule as some residues but it is not contiguous
(or at least I got it like that)

1) easy and dirty: switch back to a non-bonded ZN-finger description:
in the few hudreds of picoseconds of the QM/MM run the system will
(probably) not fall apart
2) long and clean: take one of the four Zn-finger ligand residues,
generate a new non-standard residue containing it and the zinc (put
the bond while generating the lib or the prepi file), and then when
loading the pdb with leap add the other 3 bonds between the zinc (now
part of the first ligand residue) and the other 3 ligand residues
(remember now the Zn does not go after the end of the chain, but it is
part of the chain, being embedded in the new non-standard residue)

That should solve the problem (the first does for sure, the second
needs to be proven for other cases)

I hope it helped.

On Jun 30, 7:04 pm, Teodoro Laino <teodor... at> wrote:
> Let me stress a couple of things:
> 1) the keyword exists! you should be able to find it.
> 2) the reason for this error is not the one mentioned by you. The reason is again written in the original message: atoms in a same molecule MUST be contiguous.
> In any case messages without an example (that can be used to identify and possibly fix any error) have to be considered just as spam.
> Best regards,
> Teo
> On Jun 30, 2011, at 4:14 PM, Papy wrote:
> > Ok,
> > So the problem was that I add 4 bounds in my tleap file with amber.
> > (For a Zinc Finger). It is impossible to add explicitely bond in the
> > topology, because CP2K cannot read them.
> > Thanks for your help.
> > Best
> > Christophe
> > --
> > You received this message because you are subscribed to the Google Groups "cp2k" group.
> > To post to this group, send email to cp... at
> > To unsubscribe from this group, send email to cp2k+uns... at
> > For more options, visit this group at

More information about the CP2K-user mailing list