Antwort: [CP2K:3344] ERROR in topology_generate_molecule

marco.stenta marco.... at gmail.com
Fri Jul 1 00:33:43 CEST 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
REORDER in
FORCE_EVAL / SUBSYS / TOPOLOGY / GENERATE

Not impossible to find but, if I may say, the error message referring
to REORDERING was slightly misleading.
http://cp2k.berlios.de/manual/CP2K_INPUT/FORCE_EVAL/SUBSYS/TOPOLOGY/GENERATE.html#desc_REORDER

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
readers:
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
Cterm
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)

Solution:
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.
cheers
m

On Jun 30, 7:04 pm, Teodoro Laino <teodor... at gmail.com> 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
>
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