[CP2K:610] Re: How do I generate PSF ?

[Teodoro Laino]

For not particularly "exotic"  geometries CP2K should be able to get  
the proper connectivity.
What you've seen could be some sort of bug or wrong parameters in input.
Can you please post all the necessary file to reproduce the error  
(input file and PDB) ?
does it hang infinitely?

teo

On 20 Jan 2008, at 23:34, Jack Shultz wrote:

> Thanks Shawn,
>
> Before I go off and download that. I notice that CP2K CONNECTIVITY  
> has a default GENERATE
> GENERATE: Use a simple distance criteria. (Look at keyword BONDPARM)
> I may be runing while should be walking...trying to create an  
> CI_NEB for 2 H2O2-->2H2O+O2
> I tried GENERATE like so
>
> &TOPOLOGY
> CHARGE_BETA
>
> COORD_FILE_NAME 2H2O.pdb
>
> COORDINATE PDB
>
> CONNECTIVITY GENERATE
>
> &END TOPOLOGY
>
> This gets a little bit hung on Generate
>
>  GENERATE|  Number of Torsions  
> generated:                                      2
>  GENERATE|  Number of Impropers  
> generated:                                     0
>  GENERATE|  Number of 1-4 interactions  
> generated:                              2
>
> Would you recomend generating with the plugin then or should I be  
> able to do it with CP2K
>
> On Jan 20, 2008 5:18 PM, Shawn T. Brown <shawn... at gmail.com> wrote:
> The programs VMD and  NAMD has a program called psfgen.  Check out  
> the website http://www.ks.uiuc.edu/Research/vmd/plugins/psfgen/ for  
> info.
>
> Cheers,
> Shawn
>
>
>
> On Jan 20, 2008 5:11 PM, Jack Shultz <jackyg... at gmail.com> wrote:
> Is there any GPL software for generating PSF ?
>
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