[CP2K:2755] Re: Using AMBER prmtop in cp2k for both FF parameters and connectivity

[Laino Teodoro]

I will - hold on.

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/manualfor further 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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