[CP2K:1013] Re: input coordinates & charges

Csilla Varnai cv... at cam.ac.uk
Wed May 7 16:09:54 UTC 2008

Dear Teo,

Thanks very much!
Best regards,


On 7 May 2008, at 17:04, Teodoro Laino wrote:

> Dear Csilla,
> you got exactly the point.
> In CP2K we take the CHARMM convention where a type has associated a  
> charge.
> This is different from AMBER where the same type can have different  
> charges.
> So the best thing to do is to redefine your types according the  
> convention that a type
> has a well defined charge (this most of the times is terribly easy..  
> just append a letter or a number to
> the existing type).
> Cheers
> Teo
> p.s.: even with PDB this won't necessarily work. I'm not TOTALLY  
> sure but  in case you define two different
> charges for the same type, only the first one may be assigned to  
> that type. The result is that the
> charges of your system will be wrong. I will add a warning for  
> handling this exception, though reading
> the charges from the beta column of the PDB is not something really  
> standard.
> On 7 May 2008, at 17:55, Csilla Varnai wrote:
>> in case of peptides. Hence, I need to read in the charges. I have
>> found only 1 way to do it so far, namely reading it from a PDB file.
>> My problem is that in this case I loose the accuracy of the
>> coordinates, since this format is fairly restricted and I cannot read
>> the coordinates only at a +/-0.001 level.
>> Could anyone please help me, if there is a better way I've missed to
>> get both the charges and the coordinates at a given accuracy?
> >

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