[CP2K:3406] ERROR in topology_generate_molecule

Teodoro Laino teodor... at gmail.com
Fri Aug 5 09:53:11 UTC 2011

Very probably your PSF is fault.

You have two options (actually only 1 if you need a topology):

1) fix your psf (keeping in mind that cp2k requires atoms in the same molecule to be contiguous) 


2) if you do NOT need a topology just read the pdb and connectivity OFF.


On Aug 5, 2011, at 11:45 AM, Nikita wrote:

> Dear CP2K users and developers,
> I'm trying to run a MM simulation on a quartz surface. I've checked
> carefully my input file, but I can't find the solution to this error:
> *** Detected a non contiguous molecule!! Too late at this stage  ***
> *** everything should be already ordered! Try with the keyword   ***
> *** reordering.. It may help!                                    ***
> I'm using x-plor psf and a pdb file.
> I've also tried to use the REORDER keyword but it does not work.
> Could you please suggest me how to overcome this problem.
> Thank you very much in advance,
> Nikita
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