Using AMBER prmtop in cp2k for both FF parameters and connectivity

Ilyas Khaliullin khal... at gmail.com
Fri Jun 11 14:58:05 CEST 2010


Seems like next doesn't work for me:

  &MM
    &FORCEFIELD
       PARMTYPE AMBER
       PARM_FILE_NAME ahx.prmtop
    &END FORCEFIELD
    &POISSON
      &EWALD
        EWALD_TYPE SPME
        GMAX 50 50 50
      &END EWALD
    &END POISSON
  &END MM
  &SUBSYS
    &CELL
      ABC 60.0 60.0 60.0
    &END CELL
    &TOPOLOGY
      CONN_FILE_FORMAT AMBER
      CONN_FILE_NAME ahx.prmtop
      COORD_FILE_FORMAT PDB
      COORD_FILE_NAME ahx.conv.pdb
    &END TOPOLOGY
  &END SUBSYS

CP2K hangs after printing some CELL related information.
I've uploaded my input, structure and prmtop files here as
http://groups.google.com/group/cp2k/web/AHX.tgz
Could anyone, please, look through them and give me some advices?

On 11 июн, 14:54, Teodoro Laino <teodor... at gmail.com> wrote:
> CP2K reads natively AMBER top files (both for FF and conn). Seehttp://cp2k.berlios.de/manualfor further info.
> Regards,
> Teo
>
>
>
> Ilyas Khaliullin wrote:
> > Dear colleagues!
> > I'm new to cp2k and planning to do some QM/MM calculations with it.
> > So i started with a simple geometry optimization of a small protein of
> > interest and created prmtop file for it with AmberTools 1.3. &QMMM
> > input section has been created by gen-cp2k-qmmm.py script I found here
> > (many thanks to the author!).
> > But all my calculation attempts failed with "Missing critical
> > ForceField parameters!" error.
> > I think that is due to somehow mistaken connectivity generation which
> > builds extra bonds and/or angles.
> > So the question is: is it possible for cp2k to take connectivity
> > information directly from AMBER prmtop or, if it's not, how can I
> > convert prmtop to psf-file to specify connectivity explicitly?
>
> > Thanks in advance,
> > Ilyas.


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