Using AMBER prmtop in cp2k for both FF parameters and connectivity

[Ilyas Khaliullin]

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.

[Teodoro Laino]

CP2K reads natively AMBER top files (both for FF and conn). See
http://cp2k.berlios.de/manual for further info.
Regards,
Teo

[Ilyas Khaliullin]

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...@gmail.com> wrote:
> CP2K reads natively AMBER top files (both for FF and conn). Seehttp://cp2k.berlios.de/manualfor further info.

[Laino Teodoro]

I will - hold on.

Teo

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[Laino Teodoro]

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:

[Ilyas Khaliullin]

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.

> >> Seehttp://cp2k.berlios.de/manualforfurther info.

[Teodoro Laino]

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...@laino.eu
teodor...@gmail.com
---------------------------------------------

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[Ilyas Khaliullin]

I will.
Thanks again!
Ilyas.

On 16 июн, 17:08, Teodoro Laino <teodoro.la...@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...@laino.eu
>               teodoro.la...@gmail.com
> ---------------------------------------------