Using AMBER prmtop in cp2k for both FF parameters and connectivity
khal... at gmail.com
Wed Jun 16 12:41:54 UTC 2010
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
*** err=-300 condition FAILED at line
I'm using the same input I uploaded here.
On 15 июн, 23:35, Laino Teodoro <teodor... at gmail.com> wrote:
> thanks for reporting this issue. The bug fix is now available in the
> Best Regards,
> 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
> > 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.
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