Using AMBER prmtop in cp2k for both FF parameters and connectivity

Ilyas Khaliullin khal... at gmail.com
Thu Jun 17 08:38:39 CEST 2010


I will.
Thanks again!
Ilyas.

On 16 июн, 17:08, Teodoro Laino <teodor... at gmail.com> wrote:
> Your input is wrong - check CAREFULLY the indexes of the QM atoms and  
> the MM ones.
>
> Teo
>
> ---------------------------------------------
> Teodoro Laino
> Zurich Switzerland
>
> Contact info:
> Tel.:    http://www.jajah.com/Teo
> E-mail: teo... at laino.eu
>               teodor... at gmail.com
> ---------------------------------------------
>
> On 16 Jun 2010, at 14:41, Ilyas Khaliullin <khal... at gmail.com> wrote:
>
>
>
> > Hi!
> > Thank you!
> > Now with CVS version 2.1.283 pure MM calculation seems to work fine,
> > but QMMM attempts crush with
> > *
> > *** 12:48:28 ERRORL2 in qmmm_init:setup_qm_atom_list processor
> > 0   ***
> > *** err=-300  condition FAILED at line
> > 882                              ***
> > *
> > I'm using the same input I uploaded here.
>
> > Regards,
> > Ilyas.
>
> > On 15 июн, 23:35, Laino Teodoro <teodor... at gmail.com> wrote:
> >> Hi,
>
> >> thanks for reporting this issue. The bug fix is now available in the
> >> CVS.
> >> Best Regards,
> >> Teo
>
> >> On 11 Jun 2010, at 14:58, Ilyas Khaliullin wrote:
>
> >>> 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/manualforfurtherinfo.
> >>>> 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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