[CP2K:1013] Re: input coordinates & charges

Csilla Varnai cv... at cam.ac.uk
Mon May 12 10:19:42 UTC 2008

Dear all,

I have redefined the atomic types, and regenerated the CHARMM22  
potential file according to the new atomic types, at first sight in a  
very simple-minded way, substituting all the possible new atomic types  
(say, CC1, CC2) into the old ones (CC). But in this case, due to the  
large potential file, running the program is hopeless.
I must confess I have not tried the VMD psfgen, since I would like to  
invoke CP2K from another program, and that is the reason why I would  
like to avoid the use of other programs like the VMD psfgen. If I used  
the cp2k f77_interface, would it make any difference concerning to  
this problem? Should I also have a potential file containing atomic  
types with unambiguously defined charges? If that is the case then I  
run into the same memory problem. Does the psfgen seem to be the only  
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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