[CP2K-user] [CP2K:16867] Re: Using AMBER prmtop in cp2k for both FF parameters and connectivity
Pedro R. Figueiredo
pedrorf93 at gmail.com
Tue Apr 19 19:13:09 UTC 2022
Hi,
I am facing the same problem in CP2K 8.2. I have the prmtop file present in
that same folder:
* ********************************************************************************
* * ___
* * / \
* * [ABORT]
* * \___/ Force field file missing
* * |
* * O/|
* * /| |
* * / \
force_fields.F:146
* *******************************************************************************=====
Routine Calling Stack ===== 4 force_field_control 3
fist_init 2 qmmm_env_create 1 CP2K*
Here is my input MM section:
*&MM !
Parameters to run a MM calculation &FORCEFIELD
! Set up a force_field for the classical calculations
PARMTYPE AMBER ! Kind of torsion potential
PARM_FILE_NAME topol_LJ.prmtop ! Filename that contains the parameters of
the FF &SPLINE !
Parameters to set up the splines used in the nonboned interactions
EMAX_SPLINE 1.0E8 ! Maximum value of the potential
up to which splines will be constructed RCUT_NB [angstrom] 10
! Cutoff radius for nonbonded interactions &END SPLINE
&END FORCEFIELD &POISSON &EWALD
! Ewald parameters controlling electrostatic EWALD_TYPE
PME ! Type of ewald ALPHA .40
! Alpha parameter associated with Ewald
(EWALD|PME|SPME) ! GMAX 80
! Number of grid points (SPME and EWALD) &END EWALD &END POISSON
&END MM*
Thank you in advance!
Pedro
A quinta-feira, 17 de junho de 2010 à(s) 07:38:39 UTC+1, Ilyas Khaliullin
escreveu:
> I will.
> Thanks again!
> Ilyas.
>
> On 16 июн, 17:08, Teodoro Laino <teodoro.la... 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: teod... at laino.eu
> > teodoro.la... at gmail.com
> > ---------------------------------------------
> >
> > On 16 Jun 2010, at 14:41, Ilyas Khaliullin <khali... 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 <teodoro.la... 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 <teodoro.la... 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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