[CP2K:2762] Re: Using AMBER prmtop in cp2k for both FF parameters and connectivity

[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... at laino.eu
              teodor... at gmail.com
---------------------------------------------

On 16 Jun 2010, at 14:41, Ilyas Khaliullin <khal... 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 <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.
>
> -- 
> 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+uns... at googlegroups.com 
> .
> For more options, visit this group at http://groups.google.com/group/cp2k?hl=en 
> .
>