Using AMBER prmtop in cp2k for both FF parameters and connectivity

Ilyas Khaliullin khal... at gmail.com
Wed Jun 16 14:41:54 CEST 2010


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/manualforfurther 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.
>
> > --
> > You received this message because you are subscribed to the Google  
> > Groups "cp2k" group.
> > To post to this group, send email to cp... at googlegroups.com.
> > To unsubscribe from this group, send email to cp2k
> > +unsub... at googlegroups.com.
> > For more options, visit this group athttp://groups.google.com/
> > group/cp2k?hl=en.


More information about the CP2K-user mailing list