[CP2K:6155] Basis Sets and Kinds and Amber

[Teodoro Laino]

In QMMM, some atom names have the _QM appended (if I remember correctly), basically their name is modified compared to the classical ones.
To find it out the correct names, run enabling the proper print section (or alternatively a print_level medium should do that work for you).


> On 24 Feb 2015, at 17:59, Rolf David <rolf.d... at gmail.com> wrote:
> 
> Hi all,
> 
> I'm working on a QM/MM calculation
> I use as coord/topology/FFparamaters a amber12 restart/prmtop.
> 
> Everything is nice, except a :
> 
> *** Unknown element for KIND <OP>. This problem can be fixed specifying *** 
> *** properly elements in PDB or specifying a KIND section or getting in *** 
> *** touch with one of the developers! ***
> 
> Of course I have OP Kind in my MM and QM parts (in amber: name OP, type OP, element 8)
> (Also another SM Kind only in my MM part, i did the same as OP)
> 
> So, I put a :
> 
> &KIND OP
>  ELEMENT O
> &END KIND
>  
> In the Subsys section, also I have :
> 
> &KIND O
>  BASIS_SET 6-31Gxx
>  POTENTIAL ALL
> &END KIND
> 
> So everything went smoothly according to plan, and suddenly, I decided to change a part:
> 
> &KIND OP
>  ELEMENT O
>  BASIS_SET 6-31++Gxx
>  POTENTIAL ALL
> &END KIND
> 
> and by reading the output all oxygens (O Element) are treated as 6-31Gxx
> I change the order (&Kind O after &Kind OP) no luck.
> 
> How kind/type/element from amber interact with CP2K ?
> 
> I suppose the &KIND in the &SUBSYS are linked to the &QM_KIND in the &QMMM part, only for QMMM atoms ?
> 
> KIND OP exists only amber parm/rst file, so I needed to declare the element -> For the MM part.
> 
> But since in my &QMMM part, I only have &QM_KIND O for all my oxygens, putting a basis/potential for OP has no effect so I have to declare a &QM_KIND OP.
> By putting &QM_KIND OP, the &KIND OP basis part worked.
> 
> What about atom type (amber type, amber name, so complicated...) like for TIP3P water, O is the name, and OW is the type
> in the &QMMM part I have :
> 
> &MM_KIND OW
>  RADIUS 0.78
> &END MM_KIND
> 
> It will be applied only to MM atoms, of amber type OW ?
> 
> &KIND correspond to amber name or amber type or both or whatever it feels like it ?
> 
> Confirmations or corrections will be &KINDly appreciated.
> 
> Thanks.
> 
> 
> 
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