[CP2K:2755] Re: Using AMBER prmtop in cp2k for both FF parameters and connectivity
teodor... at gmail.com
Fri Jun 11 13:14:17 UTC 2010
I will - hold on.
On 11 Jun 2010, at 14:58, Ilyas Khaliullin wrote:
> Seems like next doesn't work for me:
> PARMTYPE AMBER
> PARM_FILE_NAME ahx.prmtop
> &END FORCEFIELD
> EWALD_TYPE SPME
> GMAX 50 50 50
> &END EWALD
> &END POISSON
> &END MM
> ABC 60.0 60.0 60.0
> &END CELL
> 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/manualfor further info.
>> 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
>>> (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
>>> 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,
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